@@ -1028,6 +1028,45 @@ describe("PullRequestSyncReactor", () => {
     ),
   );
 
+  it.effect("leaves stacks in other repositories alone when their ids match", () =>
+    Effect.scoped(
+      Effect.gen(function* () {
+        yield* TestClock.setTime(Date.parse(NOW));
+        // Without a host id the GitHub decoder falls back to the stack number, so two
+        // repositories can both report stack "3".
+        const otherLink = makeLink(7, null, {
+          repository: "owner/other",
+          url: "https://github.com/owner/other/pull/7",
+        });
+        const fixture = yield* makeHarness({
+          snapshot: makeSnapshot([makeThread("one", { pullRequests: [makeLink(1), otherLink] })]),
+          stack: (input) =>
+            Effect.succeed({
+              id: "3",
+              number: 3,
+              url: `https://github.com/${input.repository}/stack/3`,
+              base: "main",
+              layers: [
+                { number: input.number, headBranch: "layer-1", state: "open" },
+                { number: input.number + 1, headBranch: "layer-2", state: "open" },
+              ],
+            }),
+        });
+
+        yield* Effect.gen(function* () {
+          const reactor = yield* startAndSweep(fixture);
+          const firstSweep = yield* Ref.get(fixture.syncCommands);
+          yield* Ref.update(fixture.snapshots, (snapshot) => applySync(snapshot, firstSweep));
+          assert.strictEqual((yield* Ref.get(fixture.stackCalls)).length, 2);
+
+          yield* sweepAgain(fixture, reactor);
+          yield* sweepAgain(fixture, reactor);
+          assert.strictEqual((yield* Ref.get(fixture.stackCalls)).length, 2);
+        }).pipe(Effect.provide(fixture.layer));
+      }),
+    ),
+  );
+
   it.effect("keeps existing snapshots and continues when the host fails", () =>
     Effect.scoped(
       Effect.gen(function* () {
 
@@ -112,6 +112,12 @@ function stacksEqual(
   );
 }
 
+/** Stack ids are unique only within a repository, e.g. GitHub's fallback to the stack number. */
+function nativeStackKeyOf(link: ThreadPullRequestLink, stack: ThreadPullRequestStack): string {
+  const key = normalizeThreadPullRequestKey(link);
+  return `${key.host}/${key.repository}#stack:${stack.id}`;
+}
+
 function sameLayerNumbers(left: ThreadPullRequestStack, right: ThreadPullRequestStack): boolean {
   return (
     left.layers.length === right.layers.length &&
@@ -326,12 +332,17 @@ export const make = Effect.gen(function* () {
         // would keep its shorter layer list. Members of this stack whose layer list differs read
         // their stack once, in this sweep if still pending or the next; agreeing ones read none.
         if (fetched !== null) {
+          const fetchedKey = nativeStackKeyOf(first.link, fetched);
           for (const [siblingKey, siblingEntries] of groups) {
             if (siblingKey === key) continue;
             const readThisSweep = stacksReadThisSweep.get(siblingKey);
             const stale = siblingEntries.some(({ link }) => {
               const stack = readThisSweep === undefined ? link.stack : readThisSweep;
-              return stack?.id === fetched.id && !sameLayerNumbers(stack, fetched);
+              return (
+                stack !== null &&
+                nativeStackKeyOf(link, stack) === fetchedKey &&
+                !sameLayerNumbers(stack, fetched)
+              );
             });
             if (stale) retryStacks.add(siblingKey);
           }