diff --git a/api/src/org/labkey/api/data/DataRegion.java b/api/src/org/labkey/api/data/DataRegion.java
index 3aa785ea704..e5bac1b8929 100644
--- a/api/src/org/labkey/api/data/DataRegion.java
+++ b/api/src/org/labkey/api/data/DataRegion.java
@@ -1558,7 +1558,8 @@ private HtmlWriter renderNavTree(HtmlWriter out)
         final String jsObject = getJavaScriptObjectReference();
         NavTree navtree = new NavTree();
 
-        NavTree selectAll = new NavTree("Select All");
+        NavTree selectAll = new NavTree("Select All Rows");
+        selectAll.setId(getDomId() + "-navtree-select-all");
         selectAll.setScript(jsObject + ".selectAll();");
         navtree.addChild(selectAll);
 
diff --git a/api/src/org/labkey/api/data/DataRegionSelection.java b/api/src/org/labkey/api/data/DataRegionSelection.java
index ec2a3c5e1ca..acdf4b5c976 100644
--- a/api/src/org/labkey/api/data/DataRegionSelection.java
+++ b/api/src/org/labkey/api/data/DataRegionSelection.java
@@ -27,6 +27,7 @@
 import org.labkey.api.query.QueryForm;
 import org.labkey.api.query.QueryService;
 import org.labkey.api.query.QueryView;
+import org.labkey.api.util.Formats;
 import org.labkey.api.util.Pair;
 import org.labkey.api.util.SessionHelper;
 import org.labkey.api.view.ActionURL;
@@ -45,7 +46,6 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.LinkedHashSet;
-import java.util.LinkedList;
 import java.util.List;
 import java.util.Set;
 
@@ -54,8 +54,6 @@
  * Uses a synchronized Set. As per documentation on {@link Collections#synchronizedSet(Set)}, callers
  * should do their own synchronization on the set itself if they are operating on it one element at a time
  * and want to have a consistent view. This allows for the backing set to be a {@link LinkedHashSet}.
- * User: kevink
- * Date: Jan 3, 2008
  */
 public class DataRegionSelection
 {
@@ -63,6 +61,9 @@ public class DataRegionSelection
     public static final String SEPARATOR = "$";
     public static final String DATA_REGION_SELECTION_KEY = "dataRegionSelectionKey";
 
+    // Issue 53997: Establish a maximum size for query selections
+    public static final int MAX_QUERY_SELECTION_SIZE = 100_000;
+
     // set/updated using query-setSnapshotSelection
     // can be used to hold an arbitrary set of selections in session
     // example usage: set a filtered set of selected values in session
@@ -207,11 +208,9 @@ public static String getSelectionKeyFromRequest(ViewContext context)
             values = context.getRequest().getParameterValues(DataRegion.SELECT_CHECKBOX_NAME);
         if (null != values && values.length == 1 && values[0].contains("\t"))
             values = StringUtils.split(values[0],'\t');
-        List<String> parameterSelected = values == null ? new ArrayList<>() : Arrays.asList(values);
-        Set<String> result = new LinkedHashSet<>(parameterSelected);
+        Set<String> result = values == null ? new LinkedHashSet<>() : new LinkedHashSet<>(Arrays.asList(values));
 
         Set<String> sessionSelected = getSet(context, key, false);
-        //noinspection SynchronizationOnLocalVariableOrMethodParameter
         synchronized (sessionSelected)
         {
             result.addAll(sessionSelected);
@@ -268,14 +267,73 @@ public static int setSelected(ViewContext context, String key, Collection<String
      */
     public static int setSelected(ViewContext context, String key, Collection<String> selection, boolean checked, boolean useSnapshot)
     {
+        return setSelected(context, key, selection, checked, useSnapshot, false);
+    }
+
+    private static int setSelected(
+        ViewContext context,
+        String key,
+        Collection<String> selection,
+        boolean checked,
+        boolean useSnapshot,
+        boolean replaceSelection
+    )
+    {
+        if (checked && selection.size() > MAX_QUERY_SELECTION_SIZE)
+            throw new BadRequestException(selectionTooLargeMessage(selection.size()));
+
         Set<String> selectedValues = getSet(context, key, true, useSnapshot);
-        if (checked)
-            selectedValues.addAll(selection);
-        else
-            selectedValues.removeAll(selection);
+        synchronized (selectedValues)
+        {
+            if (checked)
+            {
+                if (replaceSelection)
+                {
+                    selectedValues.clear();
+                }
+                else if (selectedValues.size() + selection.size() > MAX_QUERY_SELECTION_SIZE)
+                {
+                    // Verify that adding these selections will not result in a set that is too large
+                    // Do not modify the actual selected values yet
+                    int current = selectedValues.size();
+                    int distinctAdds = 0;
+
+                    for (String id : selection)
+                    {
+                        if (!selectedValues.contains(id))
+                            distinctAdds++;
+                    }
+
+                    int prospective = current + distinctAdds;
+                    if (prospective > MAX_QUERY_SELECTION_SIZE)
+                        throw new BadRequestException(selectionTooLargeMessage(prospective));
+                }
+
+                selectedValues.addAll(selection);
+            }
+            else
+                selectedValues.removeAll(selection);
+        }
+
         return selectedValues.size();
     }
 
+    public static int setSelectedFromForm(QueryForm form)
+    {
+        var view = getQueryView(form);
+        var viewContext = view.getViewContext();
+        var selection = getSet(viewContext, form.getQuerySettings().getSelectionKey(), true);
+        var items = getSelectedItems(view, selection);
+
+        return setSelected(viewContext, form.getQuerySettings().getSelectionKey(), items, false);
+    }
+
+    private static String selectionTooLargeMessage(long size)
+    {
+        return String.format("Too many selected items: %s. Maximum number of selected items allowed is %s.",
+                Formats.commaf0.format(size), Formats.commaf0.format(MAX_QUERY_SELECTION_SIZE));
+    }
+
     /**
      * Clear any session attributes that match the given container path, as the prefix, and the selection key, as the suffix
      */
@@ -339,23 +397,21 @@ public static void clearAll(ViewContext context)
      * Gets the ids of the selected items for all items in the given query form's view.  That is,
      * not just the items on the current page, but all selected items corresponding to the view's filters.
      */
-    public static List<String> getSelected(QueryForm form, boolean clearSelected) throws IOException
+    public static Set<String> getSelected(QueryForm form, boolean clearSelected) throws IOException
     {
-        List<String> items;
         var view = getQueryView(form);
-
         var selection = getSet(view.getViewContext(), form.getQuerySettings().getSelectionKey(), true);
-        items = getSelectedItems(view, selection);
+        var items = getSelectedItems(view, selection);
 
         if (clearSelected && !selection.isEmpty())
         {
-            //noinspection SynchronizationOnLocalVariableOrMethodParameter
             synchronized (selection)
             {
                 items.forEach(selection::remove);
             }
         }
-        return Collections.unmodifiableList(items);
+
+        return Collections.unmodifiableSet(items);
     }
 
     private static Pair<DataRegion, RenderContext> getDataRegionContext(QueryView view)
@@ -399,7 +455,7 @@ private static Pair<DataRegion, RenderContext> getDataRegionContext(QueryView vi
         return schema.createView(form, null);
     }
 
-    public static List<String> getValidatedIds(@NotNull List<String> selection, QueryForm form) throws IOException
+    public static Set<String> getValidatedIds(@NotNull Collection<String> selection, QueryForm form)
     {
         return getSelectedItems(getQueryView(form), selection);
     }
@@ -446,8 +502,8 @@ public static int setSelectionForAll(QueryView view, String key, boolean checked
 
         try (Timing ignored = MiniProfiler.step("selectAll"); ResultSet rs = rgn.getResults(rc))
         {
-            var selection = createSelectionList(rc, rgn, rs, null);
-            return setSelected(view.getViewContext(), key, selection, checked);
+            var selection = createSelectionSet(rc, rgn, rs, null);
+            return setSelected(view.getViewContext(), key, selection, checked, false, true);
         }
         catch (SQLException e)
         {
@@ -460,13 +516,13 @@ public static int setSelectionForAll(QueryView view, String key, boolean checked
      * @param view the view from which to retrieve the data region context and session variable
      * @param selectedValues optionally (nullable) specify a collection of selected values that will be matched
      *                       against when selecting items. If null, then all items will be returned.
-     * @return list of items from the result set that are in the selected session, or an empty list if none.
+     * @return Set of items from the result set that are in the selected session, or an empty list if none.
      */
-    private static List<String> getSelectedItems(QueryView view, @NotNull Collection<String> selectedValues) throws IOException
+    private static Set<String> getSelectedItems(QueryView view, @NotNull Collection<String> selectedValues)
     {
         // Issue 48657: no need to query the region result set if we have no selectedValues
         if (selectedValues.isEmpty())
-            return new LinkedList<>();
+            return new LinkedHashSet<>();
 
         var dataRegionContext = getDataRegionContext(view);
         var rgn = dataRegionContext.first;
@@ -486,7 +542,7 @@ private static List<String> getSelectedItems(QueryView view, @NotNull Collection
             //noinspection SynchronizationOnLocalVariableOrMethodParameter
             synchronized (selectedValues)
             {
-                return createSelectionList(ctx, rgn, rs, selectedValues);
+                return createSelectionSet(ctx, rgn, rs, selectedValues);
             }
         }
         catch (SQLException e)
@@ -495,14 +551,14 @@ private static List<String> getSelectedItems(QueryView view, @NotNull Collection
         }
     }
 
-    private static List<String> createSelectionList(
-            RenderContext ctx,
-            DataRegion rgn,
-            ResultSet rs,
-            @Nullable Collection<String> selectedValues
+    private static Set<String> createSelectionSet(
+        RenderContext ctx,
+        DataRegion rgn,
+        ResultSet rs,
+        @Nullable Collection<String> selectedValues
     ) throws SQLException
     {
-        List<String> selected = new LinkedList<>();
+        Set<String> selected = new LinkedHashSet<>();
 
         if (rs != null)
         {
@@ -516,7 +572,11 @@ private static List<String> createSelectionList(
                 {
                     var value = rgn.getRecordSelectorValue(ctx);
                     if (selectedValues == null || selectedValues.contains(value))
+                    {
                         selected.add(value);
+                        if (selected.size() == MAX_QUERY_SELECTION_SIZE)
+                            break;
+                    }
                 }
             }
         }
diff --git a/api/src/org/labkey/api/query/QueryService.java b/api/src/org/labkey/api/query/QueryService.java
index 844b9cb3db6..bbccad189f6 100644
--- a/api/src/org/labkey/api/query/QueryService.java
+++ b/api/src/org/labkey/api/query/QueryService.java
@@ -56,6 +56,7 @@ public interface QueryService
     String EXPERIMENTAL_LAST_MODIFIED = "queryMetadataLastModified";
     String EXPERIMENTAL_PRODUCT_ALL_FOLDER_LOOKUPS = "queryProductAllFolderLookups";
     String EXPERIMENTAL_PRODUCT_PROJECT_DATA_LISTING_SCOPED = "queryProductProjectDataListingScoped";
+    String MAX_QUERY_SELECTION = "maxQuerySelection";
     String PRODUCT_FOLDERS_ENABLED = "isProductFoldersEnabled";
     String PRODUCT_FOLDERS_EXIST = "hasProductFolders";
     String USE_ROW_BY_ROW_UPDATE = "useLegacyUpdateRows";
diff --git a/api/src/org/labkey/api/view/NavTree.java b/api/src/org/labkey/api/view/NavTree.java
index aa39c319568..4faf50532ff 100644
--- a/api/src/org/labkey/api/view/NavTree.java
+++ b/api/src/org/labkey/api/view/NavTree.java
@@ -755,8 +755,13 @@ public LinkBuilder toLinkBuilder(@Nullable String cls)
             }
         }
 
+        String id = getId();
+        if (id == null)
+            id = config.makeId("popupMenuView");
+        id = id.replaceAll(" ", "");
+
         LinkBuilder builder = LinkBuilder.simpleLink(html)
-            .id(config.makeId("popupMenuView"))
+            .id(id)
             .target(getTarget())
             .title(getDescription())
             .tabindex(0)
diff --git a/api/webapp/clientapi/dom/DataRegion.js b/api/webapp/clientapi/dom/DataRegion.js
index 28899dd1ac4..2310bafd0c5 100644
--- a/api/webapp/clientapi/dom/DataRegion.js
+++ b/api/webapp/clientapi/dom/DataRegion.js
@@ -16,6 +16,7 @@ if (!LABKEY.DataRegions) {
     var ALL_ROWS_MAX = 5_000;
     var CUSTOM_VIEW_PANELID = '~~customizeView~~';
     var DEFAULT_TIMEOUT = 30_000;
+    const MAX_SELECTION_SIZE = LABKEY.moduleContext.query?.maxQuerySelection ?? 100_000;
     var PARAM_PREFIX = '.param.';
     var SORT_ASC = '+';
     var SORT_DESC = '-';
@@ -851,6 +852,11 @@ if (!LABKEY.DataRegions) {
         if (!_selDocClick) {
             _selDocClick = $(document).on('click', _onDocumentClick);
         }
+
+        // Issue 53997: Establish a maximum size for query selections
+        if (_isShowSelectAll(this)) {
+            _getNavTreeSelectAllSelector(this).html(_getSelectAllText(this));
+        }
     };
 
     var _selClickLock; // lock to prevent removing a row highlight that was just applied
@@ -910,10 +916,10 @@ if (!LABKEY.DataRegions) {
             LABKEY.DataRegion.clearSelected(config);
         }
 
-        if (this.showRows == 'selected') {
+        if (this.showRows === 'selected') {
             _removeParameters(this, [SHOW_ROWS_PREFIX]);
         }
-        else if (this.showRows == 'unselected') {
+        else if (this.showRows === 'unselected') {
             // keep "SHOW_ROWS_PREFIX=unselected" parameter
             window.location.reload(true);
         }
@@ -1035,16 +1041,31 @@ if (!LABKEY.DataRegions) {
 
             LABKEY.DataRegion.selectAll(config);
 
-            if (this.showRows === "selected") {
+            if (this.showRows === 'selected') {
                 // keep "SHOW_ROWS_PREFIX=selected" parameter
                 window.location.reload(true);
             }
-            else if (this.showRows === "unselected") {
+            else if (this.showRows === 'unselected') {
                 _removeParameters(this, [SHOW_ROWS_PREFIX]);
             }
-            else {
+            else if (this.totalRows <= MAX_SELECTION_SIZE) {
                 _toggleAllRows(this, true);
             }
+            else {
+                // The number of selected rows exceeds MAX_SELECTION_SIZE, so here we determine
+                // which rows should be checked given which page (offset) we're on.
+                const lastRowIdx = this.offset + this.rowCount;
+                if (lastRowIdx < MAX_SELECTION_SIZE) {
+                    // On a page where ALL rows are within the first MAX_SELECTION_SIZE rows,
+                    _toggleAllRows(this, true);
+                } else if (this.offset < MAX_SELECTION_SIZE && MAX_SELECTION_SIZE < lastRowIdx) {
+                    // On a page where SOME rows are within the first MAX_SELECTION_SIZE rows.
+                    _checkRows(this, MAX_SELECTION_SIZE - this.offset);
+                } else {
+                    // On a page where NONE rows are within the first MAX_SELECTION_SIZE rows.
+                    _toggleAllRows(this, false);
+                }
+            }
         }
     };
 
@@ -1079,15 +1100,15 @@ if (!LABKEY.DataRegions) {
                         var msg;
                         if (me.totalRows) {
                             if (count == me.totalRows) {
-                                msg = 'All <span class="labkey-strong">' + this.totalRows + '</span> rows selected.';
+                                msg = 'All <span class="labkey-strong">' + this.totalRows.toLocaleString() + '</span> rows selected.';
                             }
                             else {
-                                msg = 'Selected <span class="labkey-strong">' + count + '</span> of ' + this.totalRows + ' rows.';
+                                msg = 'Selected <span class="labkey-strong">' + count.toLocaleString() + '</span> of ' + this.totalRows.toLocaleString() + ' rows.';
                             }
                         }
                         else {
                             // totalRows isn't available when showing all rows.
-                            msg = 'Selected <span class="labkey-strong">' + count + '</span> rows.';
+                            msg = 'Selected <span class="labkey-strong">' + count.toLocaleString() + '</span> rows.';
                         }
                         _showSelectMessage(me, msg);
                     }
@@ -1117,7 +1138,7 @@ if (!LABKEY.DataRegions) {
     };
 
     /**
-     * Add or remove items from the selection associated with the this DataRegion.
+     * Add or remove items from the selection associated with this DataRegion.
      *
      * @param config A configuration object with the following properties:
      * @param {Array} config.ids Array of primary key ids for each row to select/unselect.
@@ -1157,7 +1178,11 @@ if (!LABKEY.DataRegions) {
             config.failure = failure;
         }
         else {
-            config.failure = function() { me.addMessage('Error sending selection.'); };
+            config.failure = function(error) {
+                let msg = 'Error setting selection';
+                if (error && error.exception) msg += ': ' + error.exception;
+                me.addMessage(msg, 'selection');
+            };
         }
 
         if (config.selectionKey) {
@@ -3037,6 +3062,7 @@ if (!LABKEY.DataRegions) {
 
         // On success, update the current selectedCount on this DataRegion and fire the 'selectchange' event
         config.success = function(data) {
+            region.removeMessage('selection');
             region.selectionModified = true;
             region.selectedCount = data.count;
             _onSelectionChange(region);
@@ -3147,20 +3173,26 @@ if (!LABKEY.DataRegions) {
         return exists;
     };
 
+    var _getDomIdSelector = function(region, suffix) {
+        let selector = '#' + region.domId;
+        if (suffix) selector += suffix;
+        return $(selector);
+    };
+
     var _getAllRowSelectors = function(region) {
         return _getFormSelector(region).find('.labkey-selectors input[type="checkbox"][name=".toggle"]');
     };
 
     var _getBarSelector = function(region) {
-        return $('#' + region.domId + '-headerbar');
+        return _getDomIdSelector(region, '-headerbar');
     };
 
     var _getContextBarSelector = function(region) {
-        return $('#' + region.domId + '-ctxbar');
+        return _getDomIdSelector(region, '-ctxbar');
     };
 
     var _getDrawerSelector = function(region) {
-        return $('#' + region.domId + '-drawer');
+        return _getDomIdSelector(region, '-drawer');
     };
 
     var _getFormSelector = function(region) {
@@ -3168,14 +3200,14 @@ if (!LABKEY.DataRegions) {
 
         // derived DataRegion's may not include the form id
         if (form.length === 0) {
-            form = $('#' + region.domId).closest('form');
+            form = _getDomIdSelector(region).closest('form');
         }
 
         return form;
     };
 
     var _getHeaderSelector = function(region) {
-        return $('#' + region.domId + '-header');
+        return _getDomIdSelector(region, '-header');
     };
 
     var _getRowSelectors = function(region) {
@@ -3183,7 +3215,7 @@ if (!LABKEY.DataRegions) {
     };
 
     var _getSectionSelector = function(region, dir) {
-        return $('#' + region.domId + '-section-' + dir);
+        return _getDomIdSelector(region, '-section-' + dir);
     };
 
     var _getShowFirstSelector = function(region) {
@@ -3198,6 +3230,10 @@ if (!LABKEY.DataRegions) {
         return $('#' + region.showAllID);
     };
 
+    var _getNavTreeSelectAllSelector = function(region) {
+        return _getDomIdSelector(region, '-navtree-select-all');
+    }
+
     // Formerly, LABKEY.DataRegion.getParamValPairsFromString / LABKEY.DataRegion.getParamValPairs
     var _getParameters = function(region, skipPrefixSet /* optional */) {
 
@@ -3321,7 +3357,7 @@ if (!LABKEY.DataRegions) {
     };
 
     var _getViewBarSelector = function(region) {
-        return $('#' + region.domId + '-viewbar');
+        return _getDomIdSelector(region, '-viewbar');
     };
 
     var _buttonSelectionBind = function(region, cls, fn) {
@@ -3542,10 +3578,22 @@ if (!LABKEY.DataRegions) {
         _setParameter(region, SHOW_ROWS_PREFIX, showRowsEnum, [OFFSET_PREFIX, MAX_ROWS_PREFIX, SHOW_ROWS_PREFIX]);
     };
 
+    var _getSelectAllText = function(region) {
+        let text = 'Select All Rows';
+        if (region.totalRows > MAX_SELECTION_SIZE) {
+            text = `Select First ${MAX_SELECTION_SIZE.toLocaleString()} Rows`;
+        }
+        return text;
+    };
+
+    var _isShowSelectAll = function(region) {
+        return region.totalRows && region.totalRows !== region.selectedCount && region.selectedCount < MAX_SELECTION_SIZE;
+    };
+
     var _showSelectMessage = function(region, msg) {
         if (region.showRecordSelectors) {
-            if (region.totalRows && region.totalRows != region.selectedCount) {
-                msg += "&nbsp;<span class='labkey-button select-all'>Select All Rows</span>";
+            if (_isShowSelectAll(region)) {
+                msg += "&nbsp;<span class='labkey-button select-all'>" + _getSelectAllText(region) + "</span>";
             }
 
             msg += "&nbsp;" + "<span class='labkey-button select-none'>Select None</span>";
@@ -3573,10 +3621,27 @@ if (!LABKEY.DataRegions) {
             }
         });
 
-        _getAllRowSelectors(region).each(function() { this.checked = checked === true; });
+        _getAllRowSelectors(region).each(function() {
+            this.checked = checked === true;
+        });
         return ids;
     };
 
+    var _checkRows = function(region, numRows) {
+        const rowSelectors = _getRowSelectors(region);
+
+        for (let i = 0; i < rowSelectors.length; i++) {
+            const el = rowSelectors[i];
+            if (!el.disabled) {
+                el.checked = i < numRows;
+            }
+        }
+
+        _getAllRowSelectors(region).each(function() {
+            this.checked = true;
+        });
+    }
+
     /**
      * Asynchronous loader for a DataRegion
      * @param region {DataRegion}
@@ -4038,8 +4103,8 @@ if (!LABKEY.DataRegions) {
         // If not all rows are visible and some rows are selected, show selection message
         if (region.totalRows && 0 !== region.selectedCount && !region.complete) {
             var msg = (region.selectedCount === region.totalRows) ?
-                        'All <span class="labkey-strong">' + region.totalRows + '</span> rows selected.' :
-                        'Selected <span class="labkey-strong">' + region.selectedCount + '</span> of ' + region.totalRows + ' rows.';
+                        'All <span class="labkey-strong">' + region.totalRows.toLocaleString() + '</span> rows selected.' :
+                        'Selected <span class="labkey-strong">' + region.selectedCount.toLocaleString() + '</span> of ' + region.totalRows.toLocaleString() + ' rows.';
             _showSelectMessage(region, msg);
         }
 
diff --git a/query/src/org/labkey/query/QueryModule.java b/query/src/org/labkey/query/QueryModule.java
index 16f6c82957c..7485cfe98ca 100644
--- a/query/src/org/labkey/query/QueryModule.java
+++ b/query/src/org/labkey/query/QueryModule.java
@@ -25,6 +25,7 @@
 import org.labkey.api.data.Aggregate;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
+import org.labkey.api.data.DataRegionSelection;
 import org.labkey.api.data.JdbcType;
 import org.labkey.api.data.views.DataViewService;
 import org.labkey.api.exp.property.PropertyService;
@@ -416,6 +417,7 @@ public JSONObject getPageContextJson(ContainerUser context)
         json.put(QueryService.PRODUCT_FOLDERS_EXIST, isProductFoldersEnabled && container.hasProductFolders());
         json.put(QueryService.EXPERIMENTAL_PRODUCT_ALL_FOLDER_LOOKUPS, QueryService.get().isProductFoldersAllFolderScopeEnabled());
         json.put(QueryService.EXPERIMENTAL_PRODUCT_PROJECT_DATA_LISTING_SCOPED, QueryService.get().isProductFoldersDataListingScopedToProject());
+        json.put(QueryService.MAX_QUERY_SELECTION, DataRegionSelection.MAX_QUERY_SELECTION_SIZE);
         return json;
     }
 }
diff --git a/query/src/org/labkey/query/controllers/QueryController.java b/query/src/org/labkey/query/controllers/QueryController.java
index 258eb3d0b91..4b37da7c7dd 100644
--- a/query/src/org/labkey/query/controllers/QueryController.java
+++ b/query/src/org/labkey/query/controllers/QueryController.java
@@ -328,6 +328,7 @@
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
@@ -6510,14 +6511,9 @@ public ApiResponse execute(final SelectForm form, BindException errors) throws E
                 DataRegionSelection.clearAll(getViewContext(), form.getKey());
                 return new DataRegionSelection.SelectionResponse(0);
             }
-            else
-            {
-                // Note: DataRegionSelection.setSelectionForAll(form, false) will query for all rows in the region to remove those in context.
-                // Instead, get the selected values in context and then "uncheck" them directly
-                List<String> currentCtxSelection = DataRegionSelection.getSelected(form, false);
-                int count = DataRegionSelection.setSelected(getViewContext(), form.getQuerySettings().getSelectionKey(), currentCtxSelection, false);
-                return new DataRegionSelection.SelectionResponse(count);
-            }
+
+            int count = DataRegionSelection.setSelectedFromForm(form);
+            return new DataRegionSelection.SelectionResponse(count);
         }
     }
 
@@ -6587,16 +6583,14 @@ public void validateForm(SelectForm form, Errors errors)
         public ApiResponse execute(final SelectForm form, BindException errors) throws Exception
         {
             getViewContext().getResponse().setHeader("Content-Type", CONTENT_TYPE_JSON);
+            Set<String> selected;
+
             if (form.getQueryName() == null)
-            {
-                Set<String> selected = DataRegionSelection.getSelected(getViewContext(), form.getKey(), form.isClearSelected());
-                return new ApiSimpleResponse("selected", selected);
-            }
+                selected = DataRegionSelection.getSelected(getViewContext(), form.getKey(), form.isClearSelected());
             else
-            {
-                List<String> selected = DataRegionSelection.getSelected(form, form.isClearSelected());
-                return new ApiSimpleResponse("selected", selected);
-            }
+                selected = DataRegionSelection.getSelected(form, form.isClearSelected());
+
+            return new ApiSimpleResponse("selected", selected);
         }
     }
 
@@ -6608,7 +6602,7 @@ public static class SetCheckAction extends MutatingApiAction<SetCheckForm>
         public ApiResponse execute(final SetCheckForm form, BindException errors) throws Exception
         {
             String[] ids = form.getId(getViewContext().getRequest());
-            List<String> selection = new ArrayList<>();
+            Set<String> selection = new LinkedHashSet<>();
             if (ids != null)
             {
                 for (String id : ids)