diff --git a/src/config/merge-patch.ts b/src/config/merge-patch.ts
index 982ccf44d1..5878fc57e1 100644
--- a/src/config/merge-patch.ts
+++ b/src/config/merge-patch.ts
@@ -2,7 +2,48 @@ import { isPlainObject } from "../utils.js";
 
 type PlainObject = Record<string, unknown>;
 
-export function applyMergePatch(base: unknown, patch: unknown): unknown {
+type MergePatchOptions = {
+  mergeObjectArraysById?: boolean;
+};
+
+function isObjectWithStringId(value: unknown): value is Record<string, unknown> & { id: string } {
+  if (!isPlainObject(value)) {
+    return false;
+  }
+  return typeof value.id === "string" && value.id.length > 0;
+}
+
+function mergeObjectArraysById(base: unknown[], patch: unknown[], options: MergePatchOptions) {
+  if (!base.every(isObjectWithStringId) || !patch.every(isObjectWithStringId)) {
+    return undefined;
+  }
+  const merged = [...base] as Array<Record<string, unknown> & { id: string }>;
+  const indexById = new Map<string, number>();
+  for (const [index, entry] of merged.entries()) {
+    indexById.set(entry.id, index);
+  }
+
+  for (const entry of patch) {
+    const existingIndex = indexById.get(entry.id);
+    if (existingIndex === undefined) {
+      merged.push(structuredClone(entry));
+      indexById.set(entry.id, merged.length - 1);
+      continue;
+    }
+    merged[existingIndex] = applyMergePatch(merged[existingIndex], entry, options) as Record<
+      string,
+      unknown
+    > & { id: string };
+  }
+
+  return merged;
+}
+
+export function applyMergePatch(
+  base: unknown,
+  patch: unknown,
+  options: MergePatchOptions = {},
+): unknown {
   if (!isPlainObject(patch)) {
     return patch;
   }
@@ -14,9 +55,16 @@ export function applyMergePatch(base: unknown, patch: unknown): unknown {
       delete result[key];
       continue;
     }
+    if (options.mergeObjectArraysById && Array.isArray(result[key]) && Array.isArray(value)) {
+      const mergedArray = mergeObjectArraysById(result[key] as unknown[], value, options);
+      if (mergedArray) {
+        result[key] = mergedArray;
+        continue;
+      }
+    }
     if (isPlainObject(value)) {
       const baseValue = result[key];
-      result[key] = applyMergePatch(isPlainObject(baseValue) ? baseValue : {}, value);
+      result[key] = applyMergePatch(isPlainObject(baseValue) ? baseValue : {}, value, options);
       continue;
     }
     result[key] = value;
diff --git a/src/gateway/server-methods/config.ts b/src/gateway/server-methods/config.ts
index e0dab1a497..807451842e 100644
--- a/src/gateway/server-methods/config.ts
+++ b/src/gateway/server-methods/config.ts
@@ -342,7 +342,9 @@ export const configHandlers: GatewayRequestHandlers = {
       );
       return;
     }
-    const merged = applyMergePatch(snapshot.config, parsedRes.parsed);
+    const merged = applyMergePatch(snapshot.config, parsedRes.parsed, {
+      mergeObjectArraysById: true,
+    });
     const schemaPatch = loadSchemaWithPlugins();
     const restoredMerge = restoreRedactedValues(merged, snapshot.config, schemaPatch.uiHints);
     if (!restoredMerge.ok) {