diff --git a/packages/app/src/stores/session-store-hooks/selectors.test.ts b/packages/app/src/stores/session-store-hooks/selectors.test.ts
index 772c44c7e..516eb594c 100644
--- a/packages/app/src/stores/session-store-hooks/selectors.test.ts
+++ b/packages/app/src/stores/session-store-hooks/selectors.test.ts
@@ -16,7 +16,11 @@ import {
   workspaceEqualityFns,
   type SidebarOrderSnapshot,
 } from "./selectors";
-import { useSessionStore, type WorkspaceDescriptor } from "../session-store";
+import {
+  useSessionStore,
+  type EmptyProjectDescriptor,
+  type WorkspaceDescriptor,
+} from "../session-store";
 
 const SERVER_ID = "test-server";
 
@@ -87,6 +91,12 @@ function emptySidebarOrder(): SidebarOrderSnapshot {
   };
 }
 
+function selectWorkspaceStructureProjectKeys(
+  state: Parameters<typeof selectWorkspaceStructureProjects>[0],
+): string[] {
+  return selectWorkspaceStructureProjects(state, SERVER_ID).map((project) => project.projectKey);
+}
+
 afterEach(() => {
   useSessionStore.getState().clearSession(SERVER_ID);
 });
@@ -208,6 +218,38 @@ describe("workspace structure composition", () => {
     });
   }
 
+  it("keeps a project parent visible throughout the last workspace archive transition", () => {
+    const workspace = createWorkspace({
+      id: "workspace-a",
+      projectId: "project-a",
+      projectDisplayName: "Project A",
+      projectRootPath: "/repo/a",
+      workspaceDirectory: "/repo/a",
+    });
+    const emptyProject: EmptyProjectDescriptor = {
+      projectId: "project-a",
+      projectDisplayName: "Project A",
+      projectCustomName: null,
+      projectRootPath: "/repo/a",
+      projectKind: "git",
+    };
+    initializeWorkspaces([workspace]);
+
+    const emittedProjectKeys = [selectWorkspaceStructureProjectKeys(useSessionStore.getState())];
+    const stop = useSessionStore.subscribe((state) => {
+      emittedProjectKeys.push(selectWorkspaceStructureProjectKeys(state));
+    });
+
+    try {
+      useSessionStore.getState().removeWorkspace(SERVER_ID, workspace.id);
+      useSessionStore.getState().addEmptyProject(SERVER_ID, emptyProject);
+    } finally {
+      stop();
+    }
+
+    expect(emittedProjectKeys).toEqual([["project-a"], ["project-a"]]);
+  });
+
   it("changes for membership updates but not status-only updates", () => {
     const workspaceA = createWorkspace({ id: "workspace-a", name: "A" });
     const workspaceB = createWorkspace({ id: "workspace-b", name: "B" });
diff --git a/packages/app/src/stores/session-store.ts b/packages/app/src/stores/session-store.ts
index 5c6c93e2d..734f700b1 100644
--- a/packages/app/src/stores/session-store.ts
+++ b/packages/app/src/stores/session-store.ts
@@ -229,6 +229,30 @@ function preserveWorkspaceMapIdentity(
   return changed ? next : existing;
 }
 
+function emptyProjectDescriptorFromWorkspace(
+  workspace: WorkspaceDescriptor,
+): EmptyProjectDescriptor {
+  return {
+    projectId: workspace.projectId,
+    projectDisplayName: workspace.projectDisplayName,
+    projectCustomName: workspace.projectCustomName ?? null,
+    projectRootPath: workspace.projectRootPath,
+    projectKind: workspace.projectKind,
+  };
+}
+
+function hasWorkspaceInProject(
+  workspaces: ReadonlyMap<string, WorkspaceDescriptor>,
+  projectId: string,
+): boolean {
+  for (const workspace of workspaces.values()) {
+    if (workspace.projectId === projectId) {
+      return true;
+    }
+  }
+  return false;
+}
+
 export type ExplorerEntryKind = "file" | "directory";
 export type ExplorerFileKind = "text" | "image" | "binary";
 export type ExplorerEncoding = "utf-8" | "base64" | "none";
@@ -1393,13 +1417,31 @@ export const useSessionStore = create<SessionStore>()(
           if (!session || !workspaceKey) {
             return prev;
           }
+          const removedWorkspace = session.workspaces.get(workspaceKey);
+          if (!removedWorkspace) {
+            return prev;
+          }
           const next = new Map(session.workspaces);
           next.delete(workspaceKey);
+          let nextEmptyProjects = session.emptyProjects;
+          if (hasWorkspaceInProject(next, removedWorkspace.projectId)) {
+            if (nextEmptyProjects.has(removedWorkspace.projectId)) {
+              nextEmptyProjects = new Map(nextEmptyProjects);
+              nextEmptyProjects.delete(removedWorkspace.projectId);
+            }
+          } else {
+            const emptyProject = emptyProjectDescriptorFromWorkspace(removedWorkspace);
+            const existing = nextEmptyProjects.get(emptyProject.projectId);
+            if (!existing || !equal(existing, emptyProject)) {
+              nextEmptyProjects = new Map(nextEmptyProjects);
+              nextEmptyProjects.set(emptyProject.projectId, emptyProject);
+            }
+          }
           return {
             ...prev,
             sessions: {
               ...prev.sessions,
-              [serverId]: { ...session, workspaces: next },
+              [serverId]: { ...session, workspaces: next, emptyProjects: nextEmptyProjects },
             },
           };
         });