diff --git a/packages/paperclip-runner/package.json b/packages/paperclip-runner/package.json
index 910453c3273..66218496966 100644
--- a/packages/paperclip-runner/package.json
+++ b/packages/paperclip-runner/package.json
@@ -181,7 +181,7 @@
     "opencode-ai": "1.18.34",
     "react-markdown": "^10.1.0",
     "remark-gfm": "^4.0.1",
-    "smol-toml": "^1.4.2"
+    "smol-toml": "^1.9.1"
   },
   "peerDependencies": {
     "react": ">=18",
diff --git a/packages/paperclip-runner/src/drivers/codex/codex-startup-trust.test.ts b/packages/paperclip-runner/src/drivers/codex/codex-startup-trust.test.ts
index e8ef76d4d72..1544e1a269d 100644
--- a/packages/paperclip-runner/src/drivers/codex/codex-startup-trust.test.ts
+++ b/packages/paperclip-runner/src/drivers/codex/codex-startup-trust.test.ts
@@ -1,3 +1,4 @@
+import { deepStrictEqual } from "node:assert";
 import {
   mkdtempSync,
   mkdirSync,
@@ -99,6 +100,61 @@ describe.each([
     },
   );
 
+  it.each(["missing", "untrusted", "trusted"])(
+    "preserves nested TOML values and sibling trust with target trust %s",
+    (trust) => {
+      const temp = realpathSync(mkdtempSync(join(tmpdir(), "codex-trust-values-")));
+      try {
+        const cwd = join(temp, "project");
+        const home = join(temp, "home");
+        mkdirSync(cwd);
+        mkdirSync(home);
+        const unrelated = [
+          'special = [nan, inf, -inf, -0.0]',
+          'created = 2026-10-12T19:04:14Z',
+          'local_date = 2026-10-12',
+          'local_time = 19:04:14',
+          '[projects."/unrelated"]',
+          'trust_level = "untrusted"',
+          'settings = { __proto__ = { keep = true }, constructor = { name = "unchanged" } }',
+          '[[mcp_servers.fixture.entries]]',
+          'name = "unchanged"',
+          '',
+        ].join("\n");
+        const target = trust === "missing" ? "" : [
+          `[projects.${JSON.stringify(cwd)}]`,
+          `trust_level = "${trust}" # retain target comment`,
+          `[projects.${JSON.stringify(cwd)}.settings]`,
+          'nested = { __proto__ = { keep = true }, values = [nan, -0.0] }',
+          '',
+        ].join("\n");
+        const original = unrelated + target;
+        writeFileSync(join(home, "config.toml"), original);
+
+        trustCodexStartupRoot(home, cwd);
+
+        const updated = readFileSync(join(home, "config.toml"), "utf8");
+        expect(updated.startsWith(unrelated)).toBe(true);
+        if (trust !== "missing") {
+          expect(updated).toBe(unrelated + target.replace(
+            'trust_level = "untrusted"', 'trust_level = "trusted"',
+          ));
+        }
+        const expected = parse(original);
+        const actual = parse(updated);
+        const projects = actual.projects as Record<string, Record<string, unknown>>;
+        expect(projects[cwd].trust_level).toBe("trusted");
+        if (trust === "missing") delete projects[cwd];
+        else projects[cwd].trust_level = trust;
+        deepStrictEqual(actual, expected);
+        trustCodexStartupRoot(home, cwd);
+        expect(readFileSync(join(home, "config.toml"), "utf8")).toBe(updated);
+      } finally {
+        rmSync(temp, { recursive: true, force: true });
+      }
+    },
+  );
+
   it("trusts the exact non-Git root and preserves unrelated config", () => {
     const temp = realpathSync(mkdtempSync(join(tmpdir(), "codex-trust-")));
     try {
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index d162c049ec4..114e61bc775 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -525,8 +525,8 @@ importers:
         specifier: ^4.0.1
         version: 4.0.1
       smol-toml:
-        specifier: ^1.4.2
-        version: 1.8.0
+        specifier: ^1.9.1
+        version: 1.9.1
     optionalDependencies:
       '@github/copilot-darwin-arm64':
         specifier: 1.0.88
@@ -1074,8 +1074,8 @@ importers:
         specifier: ^0.35.4
         version: 0.35.4(@types/node@24.13.3)
       smol-toml:
-        specifier: ^1.4.2
-        version: 1.8.0
+        specifier: ^1.9.1
+        version: 1.9.1
       ssh2:
         specifier: ^1.17.0
         version: 1.17.0
@@ -8482,8 +8482,8 @@ packages:
     engines: {node: '>=18'}
     hasBin: true
 
-  smol-toml@1.8.0:
-    resolution: {integrity: sha512-kCZr2V3ch9i00x8zXRhjUNVcjG9ijES5dDudkXvUVCT5QlJNQWElSJdZqyPemffHoLNUYwOcou0Fy+ojN0uHSQ==}
+  smol-toml@1.9.1:
+    resolution: {integrity: sha512-j7WyPdf0CJoutMzMoPLF/bVXHtKZIT9Rb4eGeEbWw8X2t5oirjPgpL+OpaENZrILYaXqYwnVH+qgUwVbl+pUJQ==}
     engines: {node: '>= 18'}
 
   sonic-boom@4.2.1:
@@ -16892,7 +16892,7 @@ snapshots:
       - bare-buffer
       - react-native-b4a
 
-  smol-toml@1.8.0: {}
+  smol-toml@1.9.1: {}
 
   sonic-boom@4.2.1:
     dependencies:
diff --git a/server/package.json b/server/package.json
index 0ce4ac72f0f..ab0bf9e23a2 100644
--- a/server/package.json
+++ b/server/package.json
@@ -107,7 +107,7 @@
     "pino-http": "^11.0.0",
     "pino-pretty": "^13.1.3",
     "sharp": "^0.35.4",
-    "smol-toml": "^1.4.2",
+    "smol-toml": "^1.9.1",
     "ssh2": "^1.17.0",
     "svix": "1.76.1",
     "ws": "^8.22.0",