diff --git a/packages/cli/src/utils/commentJson.ts b/packages/cli/src/utils/commentJson.ts
index 0b362404c4..dc97f99ed5 100644
--- a/packages/cli/src/utils/commentJson.ts
+++ b/packages/cli/src/utils/commentJson.ts
@@ -7,19 +7,164 @@
 import * as fs from 'node:fs';
 import { parse as commentJsonParse, stringify } from 'comment-json';
 export { commentJsonParse as parse, stringify };
+import { coreEvents } from '@google/gemini-cli-core';
+
+/**
+ * Type representing an object that may contain Symbol keys for comments.
+ */
+type CommentedRecord = Record<string | symbol, unknown>;
 
 /**
  * Updates a JSON file while preserving comments and formatting.
- *
- * This minimal version relies on the fact that the 'updates' object
- * already contains the comment-json metadata (Symbols) because we
- * avoided stripping them in settings.ts.
  */
 export function updateSettingsFilePreservingFormat(
   filePath: string,
   updates: Record<string, unknown>,
 ): void {
-  // Directly stringify the updates object which should have metadata
-  const updatedContent = stringify(updates, null, 2);
+  if (!fs.existsSync(filePath)) {
+    fs.writeFileSync(filePath, stringify(updates, null, 2), 'utf-8');
+    return;
+  }
+
+  const originalContent = fs.readFileSync(filePath, 'utf-8');
+
+  let parsed: Record<string, unknown>;
+  try {
+    // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
+    parsed = commentJsonParse(originalContent) as Record<string, unknown>;
+  } catch (error) {
+    coreEvents.emitFeedback(
+      'error',
+      'Error parsing settings file. Please check the JSON syntax.',
+      error,
+    );
+    return;
+  }
+
+  const updatedStructure = applyUpdates(parsed, updates);
+  const updatedContent = stringify(updatedStructure, null, 2);
+
   fs.writeFileSync(filePath, updatedContent, 'utf-8');
 }
+
+/**
+ * When deleting a property from a comment-json parsed object, relocate any
+ * leading/trailing comments that were attached to that property so they are not lost.
+ *
+ * This function re-attaches comments to the next sibling's leading comments if
+ * available, otherwise to the previous sibling's trailing comments, otherwise
+ * to the container's leading/trailing comments.
+ */
+function preserveCommentsOnPropertyDeletion(
+  container: Record<string, unknown>,
+  propName: string,
+): void {
+  const target = container as CommentedRecord;
+  const beforeSym = Symbol.for(`before:${propName}`);
+  const afterSym = Symbol.for(`after:${propName}`);
+
+  // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
+  const beforeComments = target[beforeSym] as unknown[] | undefined;
+  // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
+  const afterComments = target[afterSym] as unknown[] | undefined;
+
+  if (!beforeComments && !afterComments) return;
+
+  const keys = Object.getOwnPropertyNames(container);
+  const idx = keys.indexOf(propName);
+  const nextKey = idx >= 0 && idx + 1 < keys.length ? keys[idx + 1] : undefined;
+  const prevKey = idx > 0 ? keys[idx - 1] : undefined;
+
+  function appendToSymbol(destSym: symbol, comments: unknown[]) {
+    if (!comments || comments.length === 0) return;
+    const existing = target[destSym];
+    target[destSym] = Array.isArray(existing)
+      ? existing.concat(comments)
+      : comments;
+  }
+
+  if (beforeComments && beforeComments.length > 0) {
+    if (nextKey) {
+      appendToSymbol(Symbol.for(`before:${nextKey}`), beforeComments);
+    } else if (prevKey) {
+      appendToSymbol(Symbol.for(`after:${prevKey}`), beforeComments);
+    } else {
+      appendToSymbol(Symbol.for('before'), beforeComments);
+    }
+    delete target[beforeSym];
+  }
+
+  if (afterComments && afterComments.length > 0) {
+    if (nextKey) {
+      appendToSymbol(Symbol.for(`before:${nextKey}`), afterComments);
+    } else if (prevKey) {
+      appendToSymbol(Symbol.for(`after:${prevKey}`), afterComments);
+    } else {
+      appendToSymbol(Symbol.for('after'), afterComments);
+    }
+    delete target[afterSym];
+  }
+}
+
+/**
+ * Applies sync-by-omission semantics: synchronizes base to match desired.
+ * - Adds/updates keys from desired
+ * - Removes keys from base that are not in desired
+ * - Recursively applies to nested objects
+ * - Preserves comments when deleting keys
+ */
+function applyKeyDiff(
+  base: Record<string, unknown>,
+  desired: Record<string, unknown>,
+): void {
+  for (const existingKey of Object.getOwnPropertyNames(base)) {
+    if (!Object.prototype.hasOwnProperty.call(desired, existingKey)) {
+      preserveCommentsOnPropertyDeletion(base, existingKey);
+      delete base[existingKey];
+    }
+  }
+
+  for (const nextKey of Object.getOwnPropertyNames(desired)) {
+    const nextVal = desired[nextKey];
+    const baseVal = base[nextKey];
+
+    const isObj =
+      typeof nextVal === 'object' &&
+      nextVal !== null &&
+      !Array.isArray(nextVal);
+    const isBaseObj =
+      typeof baseVal === 'object' &&
+      baseVal !== null &&
+      !Array.isArray(baseVal);
+    const isArr = Array.isArray(nextVal);
+    const isBaseArr = Array.isArray(baseVal);
+
+    if (isObj && isBaseObj) {
+      applyKeyDiff(
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
+        baseVal as Record<string, unknown>,
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
+        nextVal as Record<string, unknown>,
+      );
+    } else if (isArr && isBaseArr) {
+      // In-place mutate arrays to preserve array-level comments on CommentArray
+      const baseArr = baseVal as unknown[];
+      const desiredArr = nextVal as unknown[];
+      baseArr.length = 0;
+      for (const el of desiredArr) {
+        baseArr.push(el);
+      }
+    } else {
+      base[nextKey] = nextVal;
+    }
+  }
+}
+
+function applyUpdates(
+  current: Record<string, unknown>,
+  updates: Record<string, unknown>,
+): Record<string, unknown> {
+  // Apply sync-by-omission semantics consistently at all levels
+  applyKeyDiff(current, updates);
+  return current;
+}