diff --git a/.changeset/project-row-isolation.md b/.changeset/project-row-isolation.md
new file mode 100644
index 00000000000..fe1129c2cc6
--- /dev/null
+++ b/.changeset/project-row-isolation.md
@@ -0,0 +1,5 @@
+---
+"kilo-code": patch
+---
+
+Keep Agent Manager worktree rows isolated when projects contain identical raw worktree IDs.
diff --git a/packages/kilo-vscode/tests/unit/agent-project-progress.test.ts b/packages/kilo-vscode/tests/unit/agent-project-progress.test.ts
index 23506c0adc5..0caddba5c5f 100644
--- a/packages/kilo-vscode/tests/unit/agent-project-progress.test.ts
+++ b/packages/kilo-vscode/tests/unit/agent-project-progress.test.ts
@@ -46,4 +46,14 @@ describe("multi-project progress state", () => {
 
     expect(store.busy().get("same")?.reason).toBe("setting-up")
   })
+
+  it("does not replace deletion progress when marking a grouped worktree", () => {
+    const store = createProjectStore("a")
+    store.applyState(state("a"))
+    store.setBusy(new Map([["same", { reason: "deleting" as const }]]))
+
+    markMultiVersionBusy(store, "a-session")
+
+    expect(store.busy().get("same")?.reason).toBe("deleting")
+  })
 })