diff --git a/apps/server/src/serverRuntimeStartup.autoPull.test.ts b/apps/server/src/serverRuntimeStartup.autoPull.test.ts
index 2bc8f31c8f8b..c1c5884fb333 100644
--- a/apps/server/src/serverRuntimeStartup.autoPull.test.ts
+++ b/apps/server/src/serverRuntimeStartup.autoPull.test.ts
@@ -163,7 +163,7 @@ it.effect("parks automatic pull until activation without delaying command readin
         }),
         Layer.mock(AnalyticsService.AnalyticsService)({ record: () => Effect.void }),
         // No provider logins or Connect link, so startup records no owners.
-        FileSystem.layerNoop({}),
+        FileSystem.layerNoop({ exists: () => Effect.succeed(true) }),
         Layer.mock(ServerSecretStore.ServerSecretStore)({ get: () => Effect.succeedNone }),
         NodeCrypto.layer,
         Layer.mock(EnvironmentAuth.EnvironmentAuth)({}),
diff --git a/apps/server/src/serverRuntimeStartup.test.ts b/apps/server/src/serverRuntimeStartup.test.ts
index 180defacbfcc..58e93da08268 100644
--- a/apps/server/src/serverRuntimeStartup.test.ts
+++ b/apps/server/src/serverRuntimeStartup.test.ts
@@ -365,3 +365,37 @@ it.effect("automatic pull only updates enabled, behind, clean default-branch che
     assert.deepStrictEqual(pulled, ["/inherited"]);
   }),
 );
+
+it.effect("startup archives active projects whose folder is gone", () =>
+  Effect.gen(function* () {
+    const archived: string[] = [];
+    const projects = {
+      update: (input: { projectId: string; archived?: boolean }) =>
+        Effect.sync(() => {
+          if (input.archived) archived.push(input.projectId);
+          return {} as never;
+        }),
+    } as unknown as ProjectService.ProjectService["Service"];
+    const fileSystem = {
+      exists: (path: string) =>
+        path === "/unreadable"
+          ? Effect.fail(new Error("EACCES") as never)
+          : Effect.succeed(path === "/present"),
+    } as unknown as FileSystem.FileSystem;
+    const project = (workspaceRoot: string, archivedAt: string | null = null) =>
+      ({ id: ProjectId.make(workspaceRoot), workspaceRoot, archivedAt }) as never;
+
+    yield* ServerRuntimeStartup.archiveMissingProjects([
+      project("/present"),
+      project("/gone"),
+      project("/already-archived", "2026-01-01T00:00:00.000Z"),
+      project("/unreadable"),
+    ]).pipe(
+      Effect.provideService(ProjectService.ProjectService, projects),
+      Effect.provideService(FileSystem.FileSystem, fileSystem),
+      Effect.provide(NodeCrypto.layer),
+    );
+
+    assert.deepStrictEqual(archived, ["/gone"]);
+  }),
+);
diff --git a/apps/server/src/serverRuntimeStartup.ts b/apps/server/src/serverRuntimeStartup.ts
index 689659ab23f5..bb2c91edeede 100644
--- a/apps/server/src/serverRuntimeStartup.ts
+++ b/apps/server/src/serverRuntimeStartup.ts
@@ -5,6 +5,7 @@ import {
   DEFAULT_SERVER_SETTINGS,
   isListedThreadLineage,
   type ModelSelection,
+  type OrchestrationProjectShell,
   type Project,
   ProjectId,
   ProviderInstanceId,
@@ -21,6 +22,7 @@ import * as Deferred from "effect/Deferred";
 import * as Effect from "effect/Effect";
 import * as Exit from "effect/Exit";
 import * as Fiber from "effect/Fiber";
+import * as FileSystem from "effect/FileSystem";
 import * as Layer from "effect/Layer";
 import * as Path from "effect/Path";
 import * as Queue from "effect/Queue";
@@ -245,6 +247,39 @@ export const autoPullProjects = Effect.fn("autoPullProjects")(function* (
   );
 });
 
+// Archive, not delete: a missing folder is often an unplugged drive, and archiving keeps threads.
+export const archiveMissingProjects = Effect.fn("archiveMissingProjects")(function* (
+  projects: ReadonlyArray<Pick<OrchestrationProjectShell, "id" | "workspaceRoot" | "archivedAt">>,
+) {
+  const fileSystem = yield* FileSystem.FileSystem;
+  const projectService = yield* ProjectService.ProjectService;
+  const random = yield* SecureRandom.SecureRandom;
+  yield* Effect.forEach(
+    projects.filter((project) => !project.archivedAt),
+    (project) =>
+      Effect.gen(function* () {
+        if (yield* fileSystem.exists(project.workspaceRoot)) return;
+        yield* projectService.update({
+          commandId: CommandId.make(yield* random.uuidV4()),
+          projectId: project.id,
+          archived: true,
+        });
+        yield* Effect.logInfo("Archived project whose folder is missing", {
+          projectId: project.id,
+          workspaceRoot: project.workspaceRoot,
+        });
+      }).pipe(
+        Effect.catch((cause) =>
+          Effect.logWarning("Failed to check project folder", {
+            projectId: project.id,
+            cause,
+          }),
+        ),
+      ),
+    { concurrency: 8, discard: true },
+  );
+});
+
 const resolveWelcomeBase = Effect.gen(function* () {
   const serverConfig = yield* ServerConfig.ServerConfig;
   const segments = serverConfig.cwd.split(/[/\\]/).filter(Boolean);
@@ -568,6 +603,9 @@ const make = Effect.fn("serverRuntimeStartup.make")(function* (options?: Startup
       "projects.auto-pull",
       Effect.gen(function* () {
         const projects = yield* (yield* ProjectStore.ProjectStoreV2).listShells();
+        yield* archiveMissingProjects(projects).pipe(
+          Effect.provideService(SecureRandom.SecureRandom, random),
+        );
         const settings = yield* serverSettings.getSettings;
         yield* autoPullProjects(projects, settings);
       }),
diff --git a/docs/user/project-settings.md b/docs/user/project-settings.md
index 8880dcb3e64c..1165b98a961a 100644
--- a/docs/user/project-settings.md
+++ b/docs/user/project-settings.md
@@ -60,6 +60,9 @@ Its threads, settings, and files stay as they are, and archived projects still s
 Settings project list, marked **Archived**. Choose one there and select **Unarchive** to bring it
 back. On mobile, both are in **Settings → Projects → Organize**.
 
+When T3 Code starts, it archives any project whose folder no longer exists, such as one you
+deleted or moved, or one on a drive that isn't connected. Unarchive it once the folder is back.
+
 A project on several machines must have every machine connected to pin or archive it.
 
 ## Worktree branch names