diff --git a/cli/src/__tests__/worktree.test.ts b/cli/src/__tests__/worktree.test.ts
index afb83f73..49c445b1 100644
--- a/cli/src/__tests__/worktree.test.ts
+++ b/cli/src/__tests__/worktree.test.ts
@@ -512,6 +512,45 @@ describe("worktree helpers", () => {
     }
   });
 
+  it("preserves repo-managed worktree checkouts when --force re-runs from the source repo", async () => {
+    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-force-preserve-"));
+    const repoRoot = path.join(tempRoot, "repo");
+    const originalCwd = process.cwd();
+
+    try {
+      fs.mkdirSync(repoRoot, { recursive: true });
+      const repoConfigDir = path.join(repoRoot, ".paperclip");
+      fs.mkdirSync(repoConfigDir, { recursive: true });
+      fs.writeFileSync(path.join(repoConfigDir, "config.json"), "stale", "utf8");
+      fs.writeFileSync(path.join(repoConfigDir, ".env"), "STALE=1", "utf8");
+
+      // Simulate the repo-managed worktrees subfolder that holds every
+      // worktree checkout (the directory PAPA-358 reported as nuked).
+      const worktreesDir = path.join(repoConfigDir, "worktrees");
+      const checkoutDir = path.join(worktreesDir, "PAP-100-feature");
+      fs.mkdirSync(checkoutDir, { recursive: true });
+      const sentinelPath = path.join(checkoutDir, "sentinel.txt");
+      fs.writeFileSync(sentinelPath, "do-not-delete", "utf8");
+
+      process.chdir(repoRoot);
+
+      await worktreeInitCommand({
+        seed: false,
+        force: true,
+        fromConfig: path.join(tempRoot, "missing", "config.json"),
+        home: path.join(tempRoot, ".paperclip-worktrees"),
+      });
+
+      expect(fs.existsSync(sentinelPath)).toBe(true);
+      expect(fs.readFileSync(sentinelPath, "utf8")).toBe("do-not-delete");
+      expect(fs.existsSync(path.join(repoConfigDir, "config.json"))).toBe(true);
+      expect(fs.readFileSync(path.join(repoConfigDir, "config.json"), "utf8")).not.toBe("stale");
+    } finally {
+      process.chdir(originalCwd);
+      fs.rmSync(tempRoot, { recursive: true, force: true });
+    }
+  });
+
   itEmbeddedPostgres(
     "seeds authenticated users into minimally cloned worktree instances",
     async () => {
diff --git a/cli/src/commands/worktree.ts b/cli/src/commands/worktree.ts
index faa8e490..fea6f2c3 100644
--- a/cli/src/commands/worktree.ts
+++ b/cli/src/commands/worktree.ts
@@ -1385,7 +1385,12 @@ async function runWorktreeInit(opts: WorktreeInitOptions): Promise<void> {
   }
 
   if (opts.force) {
-    rmSync(paths.repoConfigDir, { recursive: true, force: true });
+    // Only remove the specific files we're about to rewrite, not the whole
+    // repoConfigDir — that directory can contain sibling state such as
+    // <repo>/.paperclip/worktrees/ holding every repo-managed worktree
+    // checkout, and a recursive rmSync here would nuke them all.
+    rmSync(paths.configPath, { force: true });
+    rmSync(paths.envPath, { force: true });
     rmSync(paths.instanceRoot, { recursive: true, force: true });
   }