diff --git a/apps/desktop/src/stores/__tests__/connectionStore.oneTimeCleanup.spec.ts b/apps/desktop/src/stores/__tests__/connectionStore.oneTimeCleanup.spec.ts
index f8eebdcb7b..7ed4b0b98e 100644
--- a/apps/desktop/src/stores/__tests__/connectionStore.oneTimeCleanup.spec.ts
+++ b/apps/desktop/src/stores/__tests__/connectionStore.oneTimeCleanup.spec.ts
@@ -18,9 +18,15 @@ function installApiMocks() {
     connectDb: vi.fn().mockResolvedValue("preview-1"),
     disconnectDb: vi.fn().mockResolvedValue(undefined),
     deleteSchemaCachePrefix: vi.fn().mockResolvedValue(undefined),
+    loadConnections: vi.fn().mockResolvedValue([]),
+    loadEditorSettings: vi.fn().mockResolvedValue(null),
+    loadPinnedTreeNodeIds: vi.fn().mockResolvedValue([]),
     loadSchemaCache: vi.fn().mockResolvedValue(null),
+    loadTunnelProfiles: vi.fn().mockResolvedValue([]),
     saveConnections: vi.fn().mockResolvedValue(undefined),
+    saveEditorSettings: vi.fn().mockResolvedValue(undefined),
     saveSidebarLayout: vi.fn().mockResolvedValue(undefined),
+    loadSidebarLayout: vi.fn().mockResolvedValue(null),
     connectionDatabaseInfo: vi.fn().mockResolvedValue(undefined),
     listInstalledAgents: vi.fn().mockResolvedValue([]),
     sessionCredentialStatus: vi.fn().mockResolvedValue(false),
@@ -77,6 +83,36 @@ describe("connectionStore one_time runtime cleanup", () => {
     expect(disconnectDb).toHaveBeenCalledWith("preview-1");
   });
 
+  it("initFromDisk preserves an open one_time connection during a persisted-list reload", async () => {
+    installApiMocks();
+    const { loadConnections } = await import("@/lib/backend/api");
+    vi.mocked(loadConnections).mockResolvedValue([
+      previewConnection({ id: "saved-1", name: "Saved", one_time: false }),
+    ]);
+    const { useConnectionStore } = await import("@/stores/connectionStore");
+    const store = useConnectionStore();
+    store.connections = [previewConnection({ id: "deeplink-1", name: "Deeplink", one_time: true })];
+
+    await store.initFromDisk();
+
+    expect(store.connections.map((connection) => connection.id)).toEqual(["saved-1", "deeplink-1"]);
+    expect(store.getConfig("deeplink-1")).toMatchObject({ name: "Deeplink", one_time: true });
+  });
+
+  it("does not retain a stale saved connection removed from persisted storage", async () => {
+    installApiMocks();
+    const { loadConnections } = await import("@/lib/backend/api");
+    vi.mocked(loadConnections).mockResolvedValue([]);
+    const { useConnectionStore } = await import("@/stores/connectionStore");
+    const store = useConnectionStore();
+    store.connections = [previewConnection({ id: "removed-1", name: "Removed", one_time: false })];
+
+    await store.initFromDisk();
+
+    expect(store.getConfig("removed-1")).toBeUndefined();
+    expect(store.connections).toEqual([]);
+  });
+
   it("removeConnection leaves saved connections to the save_connections sync", async () => {
     installApiMocks();
     const { useConnectionStore } = await import("@/stores/connectionStore");
diff --git a/apps/desktop/src/stores/connectionStore.ts b/apps/desktop/src/stores/connectionStore.ts
index 6070472d87..be1c07d17c 100644
--- a/apps/desktop/src/stores/connectionStore.ts
+++ b/apps/desktop/src/stores/connectionStore.ts
@@ -8035,8 +8035,14 @@ export const useConnectionStore = defineStore("connection", () => {
         const [pinnedOrder, saved] = await Promise.all([loadPinnedTreeNodeOrder(), api.loadConnections(), tunnelProfileStore.init()]);
         setPinnedTreeNodeOrder(pinnedOrder);
         await migrateTimeoutInheritance(saved);
-        connections.value = saved.map(normalizeConnection);
-        if (connections.value.some((connection, index) => (connection.connect_timeout_inherit === true && connection.connect_timeout_secs !== saved[index]?.connect_timeout_secs) || (connection.query_timeout_inherit === true && connection.query_timeout_secs !== saved[index]?.query_timeout_secs))) {
+        const loadedConnections = saved.map(normalizeConnection);
+        const loadedIds = new Set(loadedConnections.map((connection) => connection.id));
+        // One-time deep-link connections are intentionally filtered from disk
+        // persistence. Keep them in the live list when an unrelated disk reload
+        // (for example, the scheduled-backup poll) completes while they are open.
+        const runtimeOneTimeConnections = connections.value.filter((connection) => connection.one_time === true && !loadedIds.has(connection.id));
+        connections.value = [...loadedConnections, ...runtimeOneTimeConnections];
+        if (loadedConnections.some((connection, index) => (connection.connect_timeout_inherit === true && connection.connect_timeout_secs !== saved[index]?.connect_timeout_secs) || (connection.query_timeout_inherit === true && connection.query_timeout_secs !== saved[index]?.query_timeout_secs))) {
           await persistConnections();
         }
         syncTimeoutInheritanceBackup();