@@ -11,6 +11,7 @@ import * as Path from "effect/Path";
 import * as DesktopEnvironment from "../app/DesktopEnvironment.ts";
 import * as DesktopConfig from "../app/DesktopConfig.ts";
 import * as Option from "effect/Option";
+import * as Queue from "effect/Queue";
 import * as Ref from "effect/Ref";
 import * as Stream from "effect/Stream";
 import { HttpClient, HttpClientResponse } from "effect/http";
@@ -135,7 +136,8 @@ const makeUpdateMarkerFixture = (backendMode: "native" | "WSL") =>
     const ready = yield* Deferred.make<void>();
     const runtimeChecked = yield* Deferred.make<void>();
     const markerRemoved = yield* Deferred.make<void>();
-    const exited = yield* Deferred.make<ChildProcessSpawner.ExitCode>();
+    const readyRuns = yield* Queue.unbounded<void>();
+    let nextPid = 123;
     const files = new Map([[markerPath, JSON.stringify({ startedAt: 0, expiresAt: 60_000 })]]);
     const removed: string[] = [];
     const config: DesktopBackendStartConfig = {
@@ -180,30 +182,38 @@ const makeUpdateMarkerFixture = (backendMode: "native" | "WSL") =>
           ),
       },
       spawner: ChildProcessSpawner.make(() =>
-        Effect.succeed(
-          ChildProcessSpawner.makeHandle({
-            pid: ChildProcessSpawner.ProcessId(123),
+        Effect.gen(function* () {
+          const exited = yield* Deferred.make<ChildProcessSpawner.ExitCode>();
+          const exit = Deferred.succeed(exited, ChildProcessSpawner.ExitCode(0)).pipe(
+            Effect.asVoid,
+          );
+          // Like the real spawner, closing the run's scope ends the process.
+          yield* Effect.addFinalizer(() => exit);
+          return ChildProcessSpawner.makeHandle({
+            pid: ChildProcessSpawner.ProcessId(nextPid++),
             stdout: Stream.empty,
             stderr: Stream.empty,
             all: Stream.empty,
             exitCode: Deferred.await(exited),
             isRunning: Effect.succeed(true),
-            kill: () =>
-              Deferred.succeed(exited, ChildProcessSpawner.ExitCode(0)).pipe(Effect.asVoid),
+            kill: () => exit,
             stdin: Sink.drain,
             getInputFd: () => Sink.drain,
             getOutputFd: () => Stream.empty,
             unref: Effect.succeed(Effect.void),
-          }),
-        ),
+          });
+        }),
       ),
       httpClient: HttpClient.make((request) =>
         Deferred.succeed(probeStarted, undefined).pipe(
           Effect.andThen(Deferred.await(allowReady)),
           Effect.as(HttpClientResponse.fromWeb(request, new Response(null, { status: 200 }))),
         ),
       ),
-      onReady: Deferred.succeed(ready, undefined).pipe(Effect.asVoid),
+      onReady: Deferred.succeed(ready, undefined).pipe(
+        Effect.andThen(Queue.offer(readyRuns, undefined)),
+        Effect.asVoid,
+      ),
     });
     const publishRuntime = (pid: number) =>
       files.set(
@@ -223,6 +233,7 @@ const makeUpdateMarkerFixture = (backendMode: "native" | "WSL") =>
       probeStarted,
       allowReady,
       ready,
+      readyRuns,
       runtimeChecked,
       markerRemoved,
       publishRuntime,
@@ -315,6 +326,58 @@ describe("DesktopBackendPool", () => {
     ),
   );
 
+  it.effect("leaves a replacement update marker written while an earlier wait is pending", () =>
+    Effect.scoped(
+      Effect.gen(function* () {
+        const fixture = yield* makeUpdateMarkerFixture("native");
+        yield* Effect.gen(function* () {
+          const pool = yield* DesktopBackendPool.DesktopBackendPool;
+          const primary = yield* pool.primary;
+          yield* primary.start;
+          yield* Deferred.succeed(fixture.allowReady, undefined);
+          yield* Deferred.await(fixture.ready);
+          yield* Deferred.await(fixture.runtimeChecked);
+          yield* TestClock.adjust(Duration.millis(DESKTOP_UPDATE_IN_PROGRESS_TTL_MS - 1_000));
+          const replacement = JSON.stringify({ startedAt: 59_000, expiresAt: 119_000 });
+          fixture.files.set(markerPath, replacement);
+          yield* TestClock.adjust(Duration.millis(DESKTOP_UPDATE_IN_PROGRESS_TTL_MS));
+          assert.equal(fixture.files.get(markerPath), replacement);
+          assert.deepEqual(fixture.removed, []);
+        }).pipe(Effect.provide(fixture.layer));
+      }),
+    ),
+  );
+
+  it.effect("a later backend run's readiness supersedes the earlier run's marker wait", () =>
+    Effect.scoped(
+      Effect.gen(function* () {
+        const fixture = yield* makeUpdateMarkerFixture("native");
+        yield* Effect.gen(function* () {
+          const pool = yield* DesktopBackendPool.DesktopBackendPool;
+          const primary = yield* pool.primary;
+          yield* primary.start;
+          yield* Deferred.succeed(fixture.allowReady, undefined);
+          yield* Queue.take(fixture.readyRuns);
+          yield* Deferred.await(fixture.runtimeChecked);
+          yield* TestClock.adjust(Duration.seconds(30));
+          yield* primary.stop();
+          yield* primary.start;
+          yield* Queue.take(fixture.readyRuns);
+          yield* TestClock.adjust(Duration.seconds(31));
+          assert.isTrue(
+            fixture.files.has(markerPath),
+            "the earlier run's wait must not end the later run's handoff",
+          );
+          assert.deepEqual(fixture.removed, []);
+          fixture.publishRuntime(124);
+          yield* TestClock.adjust(Duration.millis(100));
+          yield* Deferred.await(fixture.markerRemoved);
+          assert.deepEqual(fixture.removed, [markerPath]);
+        }).pipe(Effect.provide(fixture.layer));
+      }),
+    ),
+  );
+
   it.effect("unregister stops the registered instance", () =>
     Effect.scoped(
       Effect.gen(function* () {
 
@@ -7,6 +7,7 @@ import * as Deferred from "effect/Deferred";
 import * as Duration from "effect/Duration";
 import * as Effect from "effect/Effect";
 import * as Exit from "effect/Exit";
+import * as FiberHandle from "effect/FiberHandle";
 import * as Layer from "effect/Layer";
 import * as Option from "effect/Option";
 import * as Schedule from "effect/Schedule";
@@ -138,7 +139,8 @@ export const layer = Layer.effect(
       httpBaseUrl: URL,
       pid: number,
     ) {
-      if (!(yield* fileSystem.exists(updateMarkerPath).pipe(Effect.orElseSucceed(() => false)))) {
+      const marker = yield* fileSystem.readFileString(updateMarkerPath).pipe(Effect.option);
+      if (Option.isNone(marker)) {
         return;
       }
       yield* fileSystem.readFileString(serverRuntimePath).pipe(
@@ -151,8 +153,14 @@ export const layer = Layer.effect(
         }),
         Effect.timeoutOption(Duration.millis(DESKTOP_UPDATE_IN_PROGRESS_TTL_MS)),
       );
-      yield* fileSystem.remove(updateMarkerPath, { force: true }).pipe(Effect.ignore);
+      // A later update may have replaced the marker; that handoff is not ours to end.
+      const current = yield* fileSystem.readFileString(updateMarkerPath).pipe(Effect.option);
+      if (Option.isSome(current) && current.value === marker.value) {
+        yield* fileSystem.remove(updateMarkerPath, { force: true }).pipe(Effect.ignore);
+      }
     });
+    // One wait at a time: each run's shutdown or readiness ends the previous run's wait.
+    const updateMarkerWait = yield* FiberHandle.make<void>();
 
     // Persist fatal Windows fallbacks; transient transport failures must preserve the user's WSL preference.
     const handlePrimaryPreflightFailure = Effect.fn("desktop.backendPool.primaryPreflightFailed")(
@@ -201,8 +209,7 @@ export const layer = Layer.effect(
       configResolve: configuration.resolvePrimary,
       // Absorb window errors so readiness can reset restartAttempt.
       onReady: (httpBaseUrl, pid) =>
-        releaseUpdateMarker(httpBaseUrl, pid).pipe(
-          Effect.forkIn(layerScope),
+        FiberHandle.run(updateMarkerWait, releaseUpdateMarker(httpBaseUrl, pid)).pipe(
           Effect.andThen(desktopWindow.handleBackendReady(httpBaseUrl)),
           // Only once the main window exists, so the recovery window never closes into nothing.
           Effect.andThen(SubscriptionRef.set(primaryBackendStartup, { _tag: "Ready" })),
@@ -214,7 +221,10 @@ export const layer = Layer.effect(
         ),
       onStartupFailure: (failure) =>
         SubscriptionRef.set(primaryBackendStartup, { _tag: "Failing", ...failure }),
-      onShutdown: () => desktopWindow.handleBackendNotReady,
+      onShutdown: () =>
+        FiberHandle.clear(updateMarkerWait).pipe(
+          Effect.andThen(desktopWindow.handleBackendNotReady),
+        ),
       onPreflightFailed: handlePrimaryPreflightFailure,
       onStateDirOwned: () =>
         electronDialog