diff --git a/apps/web/src/components/settings/ProjectSettingsPanel.logic.test.ts b/apps/web/src/components/settings/ProjectSettingsPanel.logic.test.ts
index 6f8ef830daf5c..8d0ad779842cf 100644
--- a/apps/web/src/components/settings/ProjectSettingsPanel.logic.test.ts
+++ b/apps/web/src/components/settings/ProjectSettingsPanel.logic.test.ts
@@ -1,5 +1,5 @@
 import { describe, expect, it } from "vite-plus/test";
-import { EnvironmentId, ProjectId } from "@t3tools/contracts";
+import { EnvironmentId, ProjectId, ThreadId } from "@t3tools/contracts";
 import { planProjectRemoval } from "@t3tools/client-runtime/state/projects";
 
 describe("project removal confirmation", () => {
@@ -16,18 +16,32 @@ describe("project removal confirmation", () => {
     environmentLabel: "Remote",
   };
 
-  it("limits a checkout's thread count to its environment and project", () => {
+  const parentId = ThreadId.make("parent");
+  const listed = { rootThreadId: parentId, parentThreadId: null, relationshipToParent: null };
+  const child = { rootThreadId: parentId, parentThreadId: parentId };
+
+  it("limits a checkout's thread count to its listed threads in that environment and project", () => {
     const plan = planProjectRemoval({
       members: [local],
       groupMemberCount: 2,
       hasOtherMembers: false,
       displayName: "Repo",
       threads: [
-        { environmentId: local.environmentId, projectId: local.id },
-        { environmentId: remote.environmentId, projectId: remote.id },
+        { environmentId: local.environmentId, projectId: local.id, lineage: listed },
+        {
+          environmentId: local.environmentId,
+          projectId: local.id,
+          lineage: { ...child, relationshipToParent: "subagent" },
+        },
+        {
+          environmentId: local.environmentId,
+          projectId: local.id,
+          lineage: { ...child, relationshipToParent: "fork", sideChat: true },
+        },
+        { environmentId: remote.environmentId, projectId: remote.id, lineage: listed },
       ],
     });
-    expect(plan.projectThreads).toHaveLength(1);
+    expect(plan.projectThreads).toHaveLength(3);
     expect(plan.confirmationMessage).toBe(
       'Remove checkout "Repo" and delete its 1 thread?\nPath: /work/repo\nEnvironment: Local\nThose threads and any archived threads are deleted from T3 Code. Provider sessions are kept.\nOther entries in this grouped project are unaffected.\nThis action cannot be undone.',
     );
diff --git a/packages/client-runtime/src/state/projectRemoval.ts b/packages/client-runtime/src/state/projectRemoval.ts
index 09c65a772e689..2225e5758bd2d 100644
--- a/packages/client-runtime/src/state/projectRemoval.ts
+++ b/packages/client-runtime/src/state/projectRemoval.ts
@@ -1,7 +1,9 @@
+import { isListedThreadLineage } from "@t3tools/contracts";
+
 import type { EnvironmentProject, EnvironmentThreadShell } from "./models.ts";
 
 export function planProjectRemoval<
-  Thread extends Pick<EnvironmentThreadShell, "environmentId" | "projectId">,
+  Thread extends Pick<EnvironmentThreadShell, "environmentId" | "projectId" | "lineage">,
 >(options: {
   readonly members: ReadonlyArray<
     Pick<EnvironmentProject, "id" | "environmentId" | "title" | "workspaceRoot"> & {
@@ -20,7 +22,10 @@ export function planProjectRemoval<
   const projectThreads = threads.filter((thread) =>
     memberKeys.has(`${thread.environmentId}:${thread.projectId}`),
   );
-  const threadCount = projectThreads.length + (options.unloadedThreadCount ?? 0);
+  // Side chats and subagents go with their parent but never show in thread lists.
+  const threadCount =
+    projectThreads.filter((thread) => isListedThreadLineage(thread.lineage)).length +
+    (options.unloadedThreadCount ?? 0);
   const isWholeGroup = members.length === groupMemberCount;
   const targetKind = hasOtherMembers || !isWholeGroup ? "checkout" : "project";
   const singleMember = members.length === 1 ? members[0]! : null;