diff --git a/src/config.ts b/src/config.ts
index 3d0d1a239..3d5229a71 100644
--- a/src/config.ts
+++ b/src/config.ts
@@ -2515,6 +2515,24 @@ export function claudeCodeBaselineArmed(config: OcxConfig): boolean {
   return claudeCodeBaseline.has(config);
 }
 
+/**
+ * Adopt a field-scoped Claude Code write into a long-lived config snapshot.
+ *
+ * Scoped writers commit against the current file rather than serializing the
+ * whole snapshot. Mirror that committed subtree and rebase the hand-edit guard
+ * together so a later unrelated save does not mistake the scoped write for an
+ * outstanding in-memory mutation.
+ */
+export function adoptPersistedClaudeCode(
+  config: OcxConfig,
+  persistedClaudeCode: OcxConfig["claudeCode"],
+): void {
+  config.claudeCode = structuredClone(persistedClaudeCode);
+  if (claudeCodeBaseline.has(config)) {
+    claudeCodeBaseline.set(config, structuredClone(persistedClaudeCode));
+  }
+}
+
 /**
  * Structural compare of parsed subtrees. NOT `JSON.stringify`: key order must not
  * decide whether a user's hand edit survives.
diff --git a/src/server/management/agent-settings-routes.ts b/src/server/management/agent-settings-routes.ts
index 17f7c00b3..b725e45c0 100644
--- a/src/server/management/agent-settings-routes.ts
+++ b/src/server/management/agent-settings-routes.ts
@@ -3,6 +3,7 @@ import { readFileSync } from "node:fs";
 import type { CatalogModel } from "../../codex/catalog";
 import { catalogModelSlug, invalidateCodexModelsCache, nativeModelRows, uniqueCatalogModelsForPublicList } from "../../codex/catalog";
 import {
+  adoptPersistedClaudeCode,
   DEFAULT_SUBAGENT_MODELS,
   codexAutoStartEnabled,
   hasOwnProvider,
@@ -105,12 +106,12 @@ function persistDesktopProfileField(
 ): { ok: true } | { ok: false; reason: "missing" | "invalid" | "conflict" } {
   const outcome = mutatePersistedConfig(persisted => {
     persisted.claudeCode = { ...(persisted.claudeCode ?? {}), desktopProfile };
-    return { changed: true, value: true };
+    return { changed: true, value: structuredClone(persisted.claudeCode) };
   });
   // Only mirror into memory once the durable write actually landed; an
   // `unavailable` outcome must not leave the snapshot claiming a saved profile.
   if (outcome.status === "unavailable") return { ok: false, reason: outcome.reason };
-  config.claudeCode = { ...(config.claudeCode ?? {}), desktopProfile };
+  adoptPersistedClaudeCode(config, outcome.value);
   return { ok: true };
 }
 
diff --git a/tests/native-claude-desktop-toggle.test.ts b/tests/native-claude-desktop-toggle.test.ts
index 9b1844f01..eae662448 100644
--- a/tests/native-claude-desktop-toggle.test.ts
+++ b/tests/native-claude-desktop-toggle.test.ts
@@ -4,6 +4,7 @@ import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { handleManagementAPI } from "../src/server/management-api";
 import { setIntegrationEnabled } from "../src/codex/desired-state";
+import { armClaudeCodeBaseline, saveConfigPreservingClaudeCode } from "../src/config";
 import type { ManagementApiDeps } from "../src/server/management/context";
 import type { OcxConfig } from "../src/types";
 
@@ -244,3 +245,42 @@ test("POST /apply leaves the reused server snapshot agreeing with disk", async (
   }, deps, staleSnapshot);
   expect(persistedIntent()).toBeUndefined();
 });
+
+test("POST /apply rebases the Claude hand-edit guard after its scoped profile save", async () => {
+  const snapshot = {
+    ...config(),
+    claudeCode: { authMode: "subscription" as const, nativePassthrough: true },
+  };
+  writeFileSync(join(root, "config.json"), JSON.stringify(snapshot));
+  armClaudeCodeBaseline(snapshot);
+
+  const response = await dispatch("/api/claude-desktop/apply", {
+    method: "POST",
+    headers: { "Content-Type": "application/json" },
+    body: JSON.stringify({ mode: "static" }),
+  }, {
+    fetchAllModels: async () => [],
+    writeDesktop3pConfig: () => ({ written: true, path: join(library, "applied.json"), fingerprint: "fingerprint" }),
+  }, snapshot);
+  expect(response!.status).toBe(200);
+
+  const handEdited = JSON.parse(readFileSync(join(root, "config.json"), "utf8")) as OcxConfig;
+  handEdited.claudeCode = {
+    ...handEdited.claudeCode,
+    authMode: "proxy",
+    nativePassthrough: false,
+    anthropicBaseUrl: "http://127.0.0.1:19999",
+  };
+  writeFileSync(join(root, "config.json"), JSON.stringify(handEdited));
+
+  snapshot.disabledModels = ["unrelated/model"];
+  saveConfigPreservingClaudeCode(snapshot);
+
+  const saved = JSON.parse(readFileSync(join(root, "config.json"), "utf8")) as OcxConfig;
+  expect(saved.claudeCode).toMatchObject({
+    authMode: "proxy",
+    nativePassthrough: false,
+    anthropicBaseUrl: "http://127.0.0.1:19999",
+  });
+  expect(saved.disabledModels).toEqual(["unrelated/model"]);
+});