diff --git a/src/config.ts b/src/config.ts
index 0c63a168bad..3eeec635c64 100644
--- a/src/config.ts
+++ b/src/config.ts
@@ -134,7 +134,7 @@ export {
 } from "./config/mutation-lock";
 export {
   armClaudeCodeBaseline,
-  adoptPersistedProviderIntoLiveConfig,
+  adoptPersistedClaudeCode, adoptPersistedProviderIntoLiveConfig,
   claudeCodeBaselineArmed,
   reconcileLiveConfigFromDisk,
   saveConfigPreservingClaudeCode,
diff --git a/src/config/live-reconcile.ts b/src/config/live-reconcile.ts
index 8715b1f146b..7ad249dcd6b 100644
--- a/src/config/live-reconcile.ts
+++ b/src/config/live-reconcile.ts
@@ -80,6 +80,42 @@ 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.
+ *
+ * The live subtree may already hold pending mutations a concurrent request
+ * assigned but has not saved yet — the Claude settings PUT yields between
+ * assigning `config.claudeCode` and saving. Adopt through the same three-way
+ * reconcile guarded saves use, so pending live leaves survive, disjoint
+ * committed changes merge in, and only the baseline moves wholesale to the
+ * committed subtree.
+ */
+export function adoptPersistedClaudeCode(
+  config: OcxConfig,
+  persistedClaudeCode: OcxConfig["claudeCode"],
+): void {
+  const storedBaseline: ConfigMergeValue = claudeCodeBaseline.has(config)
+    ? claudeCodeBaseline.get(config)
+    : MISSING_CONFIG_VALUE;
+  const merged = reconcileConfigValue(
+    storedBaseline === undefined ? MISSING_CONFIG_VALUE : storedBaseline,
+    config.claudeCode === undefined ? MISSING_CONFIG_VALUE : config.claudeCode,
+    persistedClaudeCode === undefined ? MISSING_CONFIG_VALUE : persistedClaudeCode,
+  );
+  if (merged === MISSING_CONFIG_VALUE) delete config.claudeCode;
+  else config.claudeCode = merged as OcxConfig["claudeCode"];
+  const baseline = liveConfigBaseline.get(config);
+  if (baseline) baseline.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 91976c144fd..61ef8997b03 100644
--- a/src/server/management/agent-settings-routes.ts
+++ b/src/server/management/agent-settings-routes.ts
@@ -6,6 +6,7 @@ import { mergeModelPinnedEfforts, modelPinnedEffortsConfigError } from "../../co
 import { MULTI_AGENT_SURFACE_ADVISORY_VERSION, multiAgentSurfaceAdvisory, resolveMultiAgentMode } from "../../config/multi-agent-surface";
 import { captureConfigTopLevelRollback, parsedConfigRebaseDeletionKeys, projectConfigRebaseProvenance } from "../../config/rebase-provenance";
 import {
+  adoptPersistedClaudeCode,
   DEFAULT_SUBAGENT_MODELS,
   codexAutoStartEnabled,
   deleteConfigTopLevelKey,
@@ -122,12 +123,12 @@ 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 };
 }
 
@@ -136,9 +137,15 @@ async function persistDesktopModeField(
   desktopMode: "first-party" | "gateway",
 ): Promise<{ ok: true } | { ok: false; reason: "missing" | "invalid" | "conflict" }> {
   const { recordClaudeDesktopMode } = await import("../../claude/desktop-first-party");
-  const outcome = mutatePersistedConfig(persisted => recordClaudeDesktopMode(persisted, desktopMode));
+  const outcome = mutatePersistedConfig(persisted => {
+    const mutation = recordClaudeDesktopMode(persisted, desktopMode);
+    return { changed: mutation.changed, value: structuredClone(persisted.claudeCode) };
+  });
   if (outcome.status === "unavailable") return { ok: false, reason: outcome.reason };
-  recordClaudeDesktopMode(config, desktopMode);
+  // First-party apply ends here — no profile-marker write follows — so without
+  // adopting, live diverges from the armed baseline and a later whole-config
+  // save reads that divergence as a pending mutation and stomps hand edits.
+  adoptPersistedClaudeCode(config, outcome.value);
   return { ok: true };
 }
 
diff --git a/tests/claude-integration/claude-desktop-first-party.test.ts b/tests/claude-integration/claude-desktop-first-party.test.ts
index 7b391f98dae..e63e17aa8dd 100644
--- a/tests/claude-integration/claude-desktop-first-party.test.ts
+++ b/tests/claude-integration/claude-desktop-first-party.test.ts
@@ -10,6 +10,7 @@ import {
   resolveClaudeDesktopMode,
 } from "../../src/claude/desktop-first-party";
 import { parseDesktopApplyArgs } from "../../src/cli/claude-desktop";
+import { armClaudeCodeBaseline, saveConfigPreservingClaudeCode } from "../../src/config";
 import { ensureClaudeDesktopMatchesDesired } from "../../src/cli/ensure-desired-integrations";
 import { handleManagementAPI } from "../../src/server/management-api";
 import { setIntegrationEnabled } from "../../src/codex/desired-state";
@@ -243,6 +244,38 @@ test("ensure warns instead of touching a gateway profile that contradicts an exp
   expect(logs.some(line => line.includes("gateway profile is still applied"))).toBe(true);
 });
 
+test("first-party apply rebases the Claude hand-edit guard after its scoped mode save", async () => {
+  // First-party apply ends at the mode-marker write — no profile-marker save
+  // follows — so unless that write adopts its committed subtree, live diverges
+  // from the armed baseline and the next whole-config save stomps a hand edit.
+  const snapshot = config({ claudeCode: { authMode: "subscription" } });
+  writeFileSync(join(root, "config.json"), JSON.stringify(snapshot));
+  armClaudeCodeBaseline(snapshot);
+
+  const applied = await dispatch("/api/claude-desktop/apply", { method: "POST" }, snapshot);
+  expect(applied.status).toBe(200);
+  expect(applied.body).toMatchObject({ mode: "first-party", saved: true });
+
+  const handEdited = JSON.parse(readFileSync(join(root, "config.json"), "utf8")) as OcxConfig;
+  handEdited.claudeCode = {
+    ...handEdited.claudeCode,
+    authMode: "proxy",
+    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",
+    anthropicBaseUrl: "http://127.0.0.1:19999",
+    desktopMode: "first-party",
+  });
+  expect(saved.disabledModels).toEqual(["unrelated/model"]);
+});
+
 test("ensure reconciles first-party env: refreshes when ON and stale, removes when OFF", () => {
   const applied = applyDesktopFirstParty(config({ port: 10300 }));
   expect(applied.ok).toBe(true);
diff --git a/tests/codex-integration/native-claude-desktop-toggle.test.ts b/tests/codex-integration/native-claude-desktop-toggle.test.ts
index 56c28ca34da..ffe20377f0d 100644
--- a/tests/codex-integration/native-claude-desktop-toggle.test.ts
+++ b/tests/codex-integration/native-claude-desktop-toggle.test.ts
@@ -6,6 +6,7 @@ import { handleManagementAPI } from "../../src/server/management-api";
 import { writeDesktop3pConfig, removeDesktop3pStandardPivot } from "../../src/claude/desktop-3p";
 import { setIntegrationEnabled } from "../../src/codex/desired-state";
 import { MANAGEMENT_JSON_BODY_MAX_BYTES } from "../../src/server/management/body";
+import { armClaudeCodeBaseline, saveConfigPreservingClaudeCode } from "../../src/config";
 import type { ManagementApiDeps } from "../../src/server/management/context";
 import type { OcxConfig } from "../../src/types";
 import { removeTreeWithRetry } from "../helpers/remove-tree";
@@ -418,3 +419,42 @@ 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"]);
+});
diff --git a/tests/config/config-user-edits.test.ts b/tests/config/config-user-edits.test.ts
index 38ac41aa378..8aef62d2073 100644
--- a/tests/config/config-user-edits.test.ts
+++ b/tests/config/config-user-edits.test.ts
@@ -4,6 +4,7 @@ import { tmpdir } from "node:os";
 import { join } from "node:path";
 import {
   armClaudeCodeBaseline,
+  adoptPersistedClaudeCode,
   adoptPersistedProviderIntoLiveConfig,
   deleteConfigTopLevelKey,
   getConfigPath,
@@ -574,6 +575,22 @@ test("our own change wins a conflict and rebases the baseline", () => {
   expect((diskConfig().claudeCode as Record<string, unknown>).authMode).toBe("proxy");
 });
 
+// A scoped Desktop write commits against the file, then adopts the committed
+// subtree. A live mutation still pending — a Claude settings PUT yields between
+// assigning `config.claudeCode` and saving — must survive the adoption and reach
+// the next save instead of being silently replaced.
+test("a scoped Claude write keeps a pending live Claude edit", () => {
+  const live = loadConfig();
+  armClaudeCodeBaseline(live);
+  live.claudeCode = { ...(live.claudeCode ?? {}), authMode: "proxy" };
+
+  adoptPersistedClaudeCode(live, { authMode: "subscription", desktopMode: "first-party" });
+
+  expect(live.claudeCode).toMatchObject({ authMode: "proxy", desktopMode: "first-party" });
+  saveConfigPreservingClaudeCode(live);
+  expect(diskConfig().claudeCode).toEqual({ authMode: "proxy", desktopMode: "first-party" });
+});
+
 test("OAuth reconciliation keeps a pending live Claude subtree authoritative", () => {
   const live = loadConfig();
   armClaudeCodeBaseline(live);