diff --git a/apps/server/src/orchestration-v2/ThreadSettlementService.test.ts b/apps/server/src/orchestration-v2/ThreadSettlementService.test.ts
index 50ac83b814626..c16c8c160e68e 100644
--- a/apps/server/src/orchestration-v2/ThreadSettlementService.test.ts
+++ b/apps/server/src/orchestration-v2/ThreadSettlementService.test.ts
@@ -8,6 +8,7 @@ import {
   ProviderInstanceId,
   RunId,
   ThreadId,
+  TurnItemId,
   type OrchestrationProjectShell,
   type OrchestrationV2AppThread,
   type OrchestrationV2Command,
@@ -598,9 +599,12 @@ const makeHarness = Effect.fn("makeThreadSettlementHarness")(function* (options:
       return next;
     });
 
-  const branchPullRequest: GitManager.GitManager["Service"]["branchPullRequest"] = (input) =>
+  const branchPullRequest: GitManager.GitManager["Service"]["branchPullRequest"] = (
+    input,
+    lookupOptions,
+  ) =>
     Ref.update(branchCalls, (calls) => [...calls, input]).pipe(
-      Effect.andThen(options.branchPullRequest?.(input) ?? Effect.succeed(null)),
+      Effect.andThen(options.branchPullRequest?.(input, lookupOptions) ?? Effect.succeed(null)),
     );
   const pullRequestSummary: PullRequestService.PullRequestService["Service"]["summary"] = (
     input,
@@ -1051,6 +1055,75 @@ describe("ThreadSettlementServiceV2 worker", () => {
     ),
   );
 
+  it.effect("settles an unlinked branch thread its agent merged from a shell, past the cache", () =>
+    Effect.scoped(
+      Effect.gen(function* () {
+        yield* TestClock.setTime(Date.parse(NOW));
+        const settled = yield* Deferred.make<void>();
+        const thread = makeThread("shell-merged", {
+          branch: "saved-feature",
+          latestUserMessageAt: DateTime.makeUnsafe("2026-08-27T00:00:00.000Z"),
+        });
+        const fixture = yield* makeHarness({
+          snapshot: makeSnapshot([thread]),
+          // The host already merged it; only a fresh read sees that past the cached open lookup.
+          branchPullRequest: (_input, lookupOptions) =>
+            Effect.succeed(makeBranchPullRequest(lookupOptions?.refresh ? "merged" : "open")),
+          onDispatch: () => Deferred.succeed(settled, undefined),
+        });
+        const at = DateTime.makeUnsafe(NOW);
+        const runId = RunId.make("run:shell-merged");
+        const runEnded: OrchestrationV2DomainEvent = {
+          type: "run.background-work-cancelled",
+          id: EventId.make("event:shell-merged:run-ended"),
+          threadId: thread.id,
+          occurredAt: at,
+          payload: { runId, restartCancelledBackgroundWork: [] },
+        };
+
+        yield* Effect.gen(function* () {
+          const reactor = yield* ThreadSettlementService.ThreadSettlementServiceV2;
+          yield* startHarness(reactor, fixture.activation, fixture.snapshotReads);
+          yield* fixture.publishEvent(runEnded);
+          yield* Queue.take(fixture.snapshotReads);
+          yield* reactor.drain;
+          assert.deepStrictEqual(yield* Ref.get(fixture.commands), []);
+
+          yield* fixture.publishEvent({
+            type: "turn-item.updated",
+            id: EventId.make("event:shell-merged:command"),
+            threadId: thread.id,
+            runId,
+            occurredAt: at,
+            payload: {
+              id: TurnItemId.make("item:shell-merged:command"),
+              threadId: thread.id,
+              runId,
+              nodeId: null,
+              providerThreadId: null,
+              providerTurnId: null,
+              nativeItemRef: null,
+              parentItemId: null,
+              ordinal: 1,
+              status: "completed",
+              title: null,
+              startedAt: at,
+              completedAt: at,
+              updatedAt: at,
+              type: "command_execution",
+              input: "gh pr merge 42 --squash",
+            },
+          });
+          yield* Deferred.await(settled);
+          assert.deepStrictEqual(
+            (yield* Ref.get(fixture.commands)).map((command) => command.threadId),
+            [thread.id],
+          );
+        }).pipe(Effect.provide(fixture.layer));
+      }),
+    ),
+  );
+
   it.effect(
     "settles branch threads on a pull request merge without waiting for the next sweep",
     () =>
diff --git a/apps/server/src/orchestration-v2/ThreadSettlementService.ts b/apps/server/src/orchestration-v2/ThreadSettlementService.ts
index a14601ae84054..35ed1d9721348 100644
--- a/apps/server/src/orchestration-v2/ThreadSettlementService.ts
+++ b/apps/server/src/orchestration-v2/ThreadSettlementService.ts
@@ -298,6 +298,9 @@ export const make = Effect.gen(function* () {
   const pullRequests = yield* PullRequestService.PullRequestService;
   const crypto = yield* Crypto.Crypto;
   const fileSystem = yield* FileSystem.FileSystem;
+  // A shell merge or close sends no event, and the branch lookup caches an open pull request for
+  // a minute, so these threads' next lookup reads the host fresh.
+  const shellClosedThreads = new Set<ThreadId>();
   const terminals = yield* TerminalManager.TerminalManager;
   const projectScripts = yield* ProjectSetupScriptRunner.ProjectSetupScriptRunner;
   // Repeated thread.settled retains settledAt; run the action only once per settlement.
@@ -490,7 +493,8 @@ export const make = Effect.gen(function* () {
       if (cwd === undefined) {
         return yield* Effect.die(new Error("thread project not found"));
       }
-      return yield* git.branchPullRequest({ cwd, branch: thread.branch });
+      const refresh = group.filter((member) => shellClosedThreads.delete(member.id)).length > 0;
+      return yield* git.branchPullRequest({ cwd, branch: thread.branch }, { refresh });
     });
 
     yield* Effect.forEach(
@@ -615,10 +619,21 @@ export const make = Effect.gen(function* () {
         return backgroundWorkHoldsCompletion(event.payload.pendingBackgroundTasks ?? [])
           ? Effect.void
           : enqueueThread(event.threadId);
-      case "turn-item.updated":
-        return turnItemUpdateCanEndBackgroundWork(event.payload)
+      case "turn-item.updated": {
+        const item = event.payload;
+        if (
+          item.type === "command_execution" &&
+          !isOrchestrationV2WorkActive(item.status) &&
+          sourceControlDefinitions.definitions.some(
+            (definition) => definition.changeRequestCloseCommand?.test(item.input) === true,
+          )
+        ) {
+          shellClosedThreads.add(event.threadId);
+        }
+        return turnItemUpdateCanEndBackgroundWork(item)
           ? enqueueThread(event.threadId)
           : Effect.void;
+      }
       case "provider-session.updated":
         return event.payload.status !== "starting" && event.payload.status !== "running"
           ? enqueueThread(event.threadId)