diff --git a/src/resources/extensions/gsd/auto-worktree.ts b/src/resources/extensions/gsd/auto-worktree.ts
index f45f5c04d..037bb516f 100644
--- a/src/resources/extensions/gsd/auto-worktree.ts
+++ b/src/resources/extensions/gsd/auto-worktree.ts
@@ -82,6 +82,10 @@ const ROOT_STATE_FILES = [
   "QUEUE.md",
   "completed-units.json",
   "metrics.json",
+  // NOTE: preferences.md is intentionally NOT in ROOT_STATE_FILES.
+  // Forward-sync (main → worktree) is handled explicitly in syncGsdStateToWorktree().
+  // Back-sync (worktree → main) must NEVER overwrite the project root's copy
+  // because the project root is authoritative for preferences (#2684).
 ] as const;
 
 /**
diff --git a/src/resources/extensions/gsd/tests/preferences-worktree-sync.test.ts b/src/resources/extensions/gsd/tests/preferences-worktree-sync.test.ts
new file mode 100644
index 000000000..04a0fbd0f
--- /dev/null
+++ b/src/resources/extensions/gsd/tests/preferences-worktree-sync.test.ts
@@ -0,0 +1,91 @@
+/**
+ * Regression tests for #2684: preferences.md must be included in both
+ * ROOT_STATE_FILES (sync) and copyPlanningArtifacts (initial seed).
+ *
+ * Without this, post_unit_hooks and all preference-driven config silently
+ * stop working inside auto-mode worktrees.
+ */
+import { test } from "node:test";
+import assert from "node:assert/strict";
+import { readFileSync, mkdtempSync, mkdirSync, writeFileSync, existsSync, rmSync } from "node:fs";
+import { join } from "node:path";
+import { tmpdir } from "node:os";
+
+test("#2684: preferences.md is NOT in ROOT_STATE_FILES (forward-only sync)", () => {
+  const srcPath = join(import.meta.dirname, "..", "auto-worktree.ts");
+  const src = readFileSync(srcPath, "utf-8");
+
+  const constIdx = src.indexOf("ROOT_STATE_FILES");
+  assert.ok(constIdx !== -1, "ROOT_STATE_FILES constant exists");
+
+  const arrayStart = src.indexOf("[", constIdx);
+  const arrayEnd = src.indexOf("] as const", arrayStart);
+  const block = src.slice(arrayStart, arrayEnd);
+
+  // preferences.md must NOT be in ROOT_STATE_FILES — it is handled separately
+  // in syncGsdStateToWorktree() (forward-only, additive). Including it in
+  // ROOT_STATE_FILES would cause syncWorktreeStateBack() to overwrite the
+  // authoritative project root copy (#2684).
+  const entries = block.split("\n")
+    .map(l => l.trim())
+    .filter(l => l.startsWith('"') && l.includes(".md"));
+  const hasPrefs = entries.some(l => l.includes("preferences.md"));
+  assert.ok(
+    !hasPrefs,
+    "preferences.md must NOT be in ROOT_STATE_FILES (back-sync would overwrite root)",
+  );
+});
+
+test("#2684: copyPlanningArtifacts file list includes preferences.md", () => {
+  const srcPath = join(import.meta.dirname, "..", "auto-worktree.ts");
+  const src = readFileSync(srcPath, "utf-8");
+
+  // Find the copyPlanningArtifacts function body
+  const fnIdx = src.indexOf("function copyPlanningArtifacts");
+  assert.ok(fnIdx !== -1, "copyPlanningArtifacts function exists");
+
+  // Extract function body (up to the next top-level function)
+  const fnBody = src.slice(fnIdx, fnIdx + 1500);
+
+  assert.ok(
+    fnBody.includes('"preferences.md"'),
+    "preferences.md should be in copyPlanningArtifacts file list",
+  );
+});
+
+test("#2684: syncGsdStateToWorktree copies preferences.md", async () => {
+  // Functional test: create a mock source and destination, call the sync
+  const srcBase = mkdtempSync(join(tmpdir(), "gsd-wt-prefs-src-"));
+  const dstBase = mkdtempSync(join(tmpdir(), "gsd-wt-prefs-dst-"));
+  const srcGsd = join(srcBase, ".gsd");
+  const dstGsd = join(dstBase, ".gsd");
+  mkdirSync(srcGsd, { recursive: true });
+  mkdirSync(dstGsd, { recursive: true });
+
+  try {
+    // Write a preferences.md in source
+    writeFileSync(
+      join(srcGsd, "preferences.md"),
+      "---\nversion: 1\n---\n\npost_unit_hooks:\n  - name: notify\n    command: echo done\n",
+    );
+
+    // Import and call syncGsdStateToWorktree
+    const { syncGsdStateToWorktree } = await import("../auto-worktree.ts");
+    syncGsdStateToWorktree(srcBase, dstBase);
+
+    // Verify preferences.md was copied
+    assert.ok(
+      existsSync(join(dstGsd, "preferences.md")),
+      "preferences.md should be copied to worktree",
+    );
+
+    const content = readFileSync(join(dstGsd, "preferences.md"), "utf-8");
+    assert.ok(
+      content.includes("post_unit_hooks"),
+      "copied preferences.md should contain the hooks config",
+    );
+  } finally {
+    rmSync(srcBase, { recursive: true, force: true });
+    rmSync(dstBase, { recursive: true, force: true });
+  }
+});