@@ -3669,7 +3669,7 @@ const makeOrchestrator = Effect.fn("orchestrationV2.Orchestrator.layer")(functio
               );
               if (!stack) return thread;
               targets = new Set(stack.layers);
-              for (const layer of existing.stack?.layers ?? []) {
+              for (const layer of stack.layers.flatMap((link) => link.stack?.layers ?? [])) {
                 const member = links.find((link) =>
                   threadPullRequestKeysEqual(link, { ...key, number: layer.number }),
                 );
 
@@ -2851,7 +2851,12 @@ it.layer(layerTest)("OrchestrationV2LayerLive lifecycle", (it) => {
           commandId: CommandId.make(`sync-${id}`),
           threadId,
           ...reference,
-          stack: reference.number === 1 || reference.number === 2 ? stack : null,
+          stack:
+            reference.number === 1 && stack
+              ? { ...stack, layers: stack.layers.filter((layer) => layer.number < 3) }
+              : reference.number === 2
+                ? stack
+                : null,
           snapshot: {
             state: "open",
             title: "PR",