diff --git a/packages/cli/src/utils/commentJson.test.ts b/packages/cli/src/utils/commentJson.test.ts
index 4957b7497..fcf2501cd 100644
--- a/packages/cli/src/utils/commentJson.test.ts
+++ b/packages/cli/src/utils/commentJson.test.ts
@@ -8,7 +8,10 @@ import { describe, it, expect, beforeEach, afterEach, vi } from 'vitest';
 import * as fs from 'node:fs';
 import * as path from 'node:path';
 import * as os from 'node:os';
-import { updateSettingsFilePreservingFormat } from './commentJson.js';
+import {
+  updateSettingsFilePreservingFormat,
+  applyUpdates,
+} from './commentJson.js';
 
 describe('commentJson', () => {
   let tempDir: string;
@@ -180,3 +183,18 @@ describe('commentJson', () => {
     });
   });
 });
+
+describe('applyUpdates', () => {
+  it('should apply updates correctly', () => {
+    const original = { a: 1, b: { c: 2 } };
+    const updates = { b: { c: 3 } };
+    const result = applyUpdates(original, updates);
+    expect(result).toEqual({ a: 1, b: { c: 3 } });
+  });
+  it('should apply updates correctly when empty', () => {
+    const original = { a: 1, b: { c: 2 } };
+    const updates = { b: {} };
+    const result = applyUpdates(original, updates);
+    expect(result).toEqual({ a: 1, b: {} });
+  });
+});
diff --git a/packages/cli/src/utils/commentJson.ts b/packages/cli/src/utils/commentJson.ts
index 9ea4d3f80..bf325d9af 100644
--- a/packages/cli/src/utils/commentJson.ts
+++ b/packages/cli/src/utils/commentJson.ts
@@ -38,7 +38,7 @@ export function updateSettingsFilePreservingFormat(
   fs.writeFileSync(filePath, updatedContent, 'utf-8');
 }
 
-function applyUpdates(
+export function applyUpdates(
   current: Record<string, unknown>,
   updates: Record<string, unknown>,
 ): Record<string, unknown> {
@@ -50,6 +50,7 @@ function applyUpdates(
       typeof value === 'object' &&
       value !== null &&
       !Array.isArray(value) &&
+      Object.keys(value).length > 0 &&
       typeof result[key] === 'object' &&
       result[key] !== null &&
       !Array.isArray(result[key])