diff --git a/desktop/src/features/channels/unreadChannelCounts.ts b/desktop/src/features/channels/unreadChannelCounts.ts
index cb33c6297..ff7bf2203 100644
--- a/desktop/src/features/channels/unreadChannelCounts.ts
+++ b/desktop/src/features/channels/unreadChannelCounts.ts
@@ -65,6 +65,32 @@ export function recordObservedUnreadEvent(
   return true;
 }
 
+// Drop observed refs for channels whose unread events the read markers now
+// fully cover. `markThreadRead`/`markMessageRead` advance a `thread:<root>`/
+// `msg:<id>` marker, but `markChannelRead`'s clearObserved prune keys these maps
+// by that synthetic key — never the real channel — so the real channel's refs
+// linger after a thread/message read covers its last badge event. A channel
+// absent from `unreadChannelIds` (and not forced or active) has no unread
+// observed events left, so its refs are dead weight. Pruning them is invisible
+// to the count (a covered channel and an absent one both contribute 0).
+export function pruneCoveredObservedRefs(
+  latestByChannel: Map<string, number>,
+  observedByChannel: Map<string, Map<string, ObservedUnreadEvent>>,
+  channelIds: Iterable<string>,
+  unreadChannelIds: ReadonlySet<string>,
+  forcedChannelIds: ReadonlySet<string>,
+  activeChannelId: string | null,
+): void {
+  for (const channelId of channelIds) {
+    if (channelId === activeChannelId) continue;
+    if (unreadChannelIds.has(channelId)) continue;
+    if (forcedChannelIds.has(channelId)) continue;
+    if (latestByChannel.get(channelId) === undefined) continue;
+    latestByChannel.delete(channelId);
+    observedByChannel.delete(channelId);
+  }
+}
+
 export function countUnreadObservedEvents(
   eventsById: ReadonlyMap<string, ObservedUnreadEvent> | undefined,
   getReadAt: (event: ObservedUnreadEvent) => number | null,
diff --git a/desktop/src/features/channels/unreadReadMarker.test.mjs b/desktop/src/features/channels/unreadReadMarker.test.mjs
index 266bca2df..1cf6b90fe 100644
--- a/desktop/src/features/channels/unreadReadMarker.test.mjs
+++ b/desktop/src/features/channels/unreadReadMarker.test.mjs
@@ -8,6 +8,7 @@ import {
   countUnreadHighPriorityObservedEvents,
   countUnreadObservedEvents,
   observedUnreadEventReadAt,
+  pruneCoveredObservedRefs,
   recordObservedUnreadEvent,
 } from "./unreadChannelCounts.ts";
 import {
@@ -388,6 +389,114 @@ test("highPriorityObservedEvents_countOnlyUnreadHighPriorityItems", () => {
   assert.equal(countUnreadHighPriorityObservedEvents(events, getReadAt), 1);
 });
 
+// --- Clearing asymmetry: prune covered observed refs ---
+
+// The headline regression. A channel was read top-level-only (channel-open) and
+// later a thread reply arrived; reading THAT thread advances thread:<root> so
+// the badge counts 0, but markChannelRead("thread:<root>") can't prune the real
+// channel's refs (wrong key). pruneCoveredObservedRefs drops the dead refs once
+// the memo no longer reports the channel unread, and the badge must STAY 0 even
+// if a catch-up REQ re-records the same already-covered event.
+test("pruneCoveredObservedRefs_threadReadCovers_prunesRefsAndBadgeStaysZero", () => {
+  const channelId = "chan";
+  const rootId = "root-1";
+  const reply = observed("reply", 500, rootId);
+  const latestByChannel = new Map([[channelId, 500]]);
+  const observedByChannel = new Map();
+  recordObservedUnreadEvent(observedByChannel, channelId, reply, 20);
+
+  // Before reading the thread: channel marker 300 < reply 500, badge counts 1.
+  const beforeRead = readAtFor(300, new Map());
+  assert.equal(
+    countUnreadBadgeObservedEvents(
+      observedByChannel.get(channelId),
+      beforeRead,
+    ),
+    1,
+  );
+
+  // Reading the thread advances thread:root-1=500. The badge now counts 0, so
+  // the memo drops the channel from unreadChannelIds — the prune signal.
+  const afterRead = readAtFor(300, new Map([[rootId, 500]]));
+  assert.equal(
+    countUnreadBadgeObservedEvents(observedByChannel.get(channelId), afterRead),
+    0,
+  );
+
+  pruneCoveredObservedRefs(
+    latestByChannel,
+    observedByChannel,
+    [channelId],
+    new Set(),
+    new Set(),
+    null,
+  );
+
+  assert.equal(latestByChannel.has(channelId), false);
+  assert.equal(observedByChannel.has(channelId), false);
+
+  // A catch-up REQ re-records the same covered event. The badge must stay 0.
+  recordObservedUnreadEvent(observedByChannel, channelId, reply, 20);
+  assert.equal(
+    countUnreadBadgeObservedEvents(observedByChannel.get(channelId), afterRead),
+    0,
+  );
+});
+
+test("pruneCoveredObservedRefs_channelStillUnread_keepsRefs", () => {
+  const channelId = "chan";
+  const latestByChannel = new Map([[channelId, 500]]);
+  const observedByChannel = new Map([[channelId, new Map()]]);
+
+  pruneCoveredObservedRefs(
+    latestByChannel,
+    observedByChannel,
+    [channelId],
+    new Set([channelId]),
+    new Set(),
+    null,
+  );
+
+  assert.equal(latestByChannel.has(channelId), true);
+  assert.equal(observedByChannel.has(channelId), true);
+});
+
+test("pruneCoveredObservedRefs_activeChannel_keepsRefs", () => {
+  const channelId = "chan";
+  const latestByChannel = new Map([[channelId, 500]]);
+  const observedByChannel = new Map([[channelId, new Map()]]);
+
+  pruneCoveredObservedRefs(
+    latestByChannel,
+    observedByChannel,
+    [channelId],
+    new Set(),
+    new Set(),
+    channelId,
+  );
+
+  assert.equal(latestByChannel.has(channelId), true);
+  assert.equal(observedByChannel.has(channelId), true);
+});
+
+test("pruneCoveredObservedRefs_forcedUnread_keepsRefs", () => {
+  const channelId = "chan";
+  const latestByChannel = new Map([[channelId, 500]]);
+  const observedByChannel = new Map([[channelId, new Map()]]);
+
+  pruneCoveredObservedRefs(
+    latestByChannel,
+    observedByChannel,
+    [channelId],
+    new Set(),
+    new Set([channelId]),
+    null,
+  );
+
+  assert.equal(latestByChannel.has(channelId), true);
+  assert.equal(observedByChannel.has(channelId), true);
+});
+
 test("addThreadActivityItems keeps newest items when input is newest-first", () => {
   const newestFirst = Array.from({ length: 101 }, (_, index) => {
     const createdAt = 100 - index;
diff --git a/desktop/src/features/channels/useUnreadChannels.ts b/desktop/src/features/channels/useUnreadChannels.ts
index f65f4bd82..f80e363be 100644
--- a/desktop/src/features/channels/useUnreadChannels.ts
+++ b/desktop/src/features/channels/useUnreadChannels.ts
@@ -12,6 +12,7 @@ import {
   makeObservedUnreadEvent,
   mapsEqual,
   observedUnreadEventReadAt,
+  pruneCoveredObservedRefs,
   recordObservedUnreadEvent,
   type ObservedUnreadEvent,
 } from "@/features/channels/unreadChannelCounts";
@@ -918,6 +919,21 @@ export function useUnreadChannels(
   const unreadChannelIdsRef = React.useRef(unreadChannelIds);
   unreadChannelIdsRef.current = unreadChannelIds;
 
+  // Drop observed refs the read markers now fully cover (the thread/message
+  // read clearing asymmetry — see pruneCoveredObservedRefs). Driven off the
+  // memo's own output; no version bump and no loop because pruning is invisible
+  // to the count.
+  React.useEffect(() => {
+    pruneCoveredObservedRefs(
+      latestByChannelRef.current,
+      observedUnreadEventsByChannelRef.current,
+      channels.map((channel) => channel.id),
+      unreadChannelIds,
+      forcedUnreadRef.current,
+      activeChannelId,
+    );
+  }, [unreadChannelIds, channels, activeChannelId]);
+
   const markAllChannelsRead = React.useCallback(() => {
     for (const channelId of unreadChannelIdsRef.current) {
       forcedUnreadRef.current.delete(channelId);