diff --git a/.changeset/agile-pandas-dance.md b/.changeset/agile-pandas-dance.md
new file mode 100644
index 000000000..5041d24ea
--- /dev/null
+++ b/.changeset/agile-pandas-dance.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 2233
+---
+**Custom STATE.md frontmatter keys are no longer dropped on every mutating verb** — syncStateFrontmatter rebuilt the frontmatter from a fixed schema, silently dropping any custom key. It now carries forward existing keys the schema does not own. (#2202)
diff --git a/src/state.cts b/src/state.cts
index 5e59b7370..f7f3811ac 100644
--- a/src/state.cts
+++ b/src/state.cts
@@ -1650,6 +1650,16 @@ function syncStateFrontmatter(content: string, cwd: string | undefined): string
     derivedFm['progress'] = normalizeProgressNumbers(existingFm['progress']);
   }
 
+  // #2202: carry forward any existing frontmatter key that the schema does not
+  // own, so custom/unknown keys are not silently dropped on every mutating verb.
+  // Schema-owned keys (already in derivedFm from buildStateFrontmatter + the
+  // preserve guards above) still win.
+  for (const key of Object.keys(existingFm)) {
+    if (!(key in derivedFm) && existingFm[key] !== undefined) {
+      derivedFm[key] = existingFm[key];
+    }
+  }
+
   const yamlStr = reconstructFrontmatter(derivedFm as unknown as Frontmatter);
   return `---\n${yamlStr}\n---\n\n${body}`;
 }
diff --git a/tests/state.test.cjs b/tests/state.test.cjs
index eaf61a34a..5257bb23d 100644
--- a/tests/state.test.cjs
+++ b/tests/state.test.cjs
@@ -611,6 +611,37 @@ milestone: v1.0
     assert.ok(!content.includes('status: unknown'), 'should not contain unknown status');
   });
 
+  test('#2202: preserves unknown frontmatter keys the schema does not own', () => {
+    // Regression: a mutating verb rewrites STATE.md via syncStateFrontmatter,
+    // which rebuilds frontmatter from the body + schema. Before #2202 it dropped
+    // any frontmatter key the schema does not own; custom/tooling keys must
+    // survive every write.
+    fs.writeFileSync(
+      path.join(tmpDir, '.planning', 'STATE.md'),
+      `---
+status: executing
+milestone: v1.0
+custom_tracking_id: ABC-123
+team: platform
+---
+
+# Project State
+
+**Current Phase:** 03
+**Current Plan:** 03-02
+`
+    );
+
+    // Any writeStateMd triggers syncStateFrontmatter.
+    runGsdTools('state update "Current Plan" "03-03"', tmpDir);
+
+    const content = fs.readFileSync(path.join(tmpDir, '.planning', 'STATE.md'), 'utf-8');
+    assert.match(content, /custom_tracking_id: ABC-123/, 'unknown key custom_tracking_id must be preserved');
+    assert.match(content, /team: platform/, 'unknown key team must be preserved');
+    // Schema-owned keys still win / survive alongside the carried-forward keys.
+    assert.ok(content.includes('status: executing'), 'schema-owned status still preserved');
+  });
+
   test('round-trip: write then read via state json', () => {
     fs.writeFileSync(
       path.join(tmpDir, '.planning', 'STATE.md'),