diff --git a/app/api/admin/__tests__/config-merge-shared.test.ts b/app/api/admin/__tests__/config-merge-shared.test.ts
new file mode 100644
index 000000000..c6f94b10e
--- /dev/null
+++ b/app/api/admin/__tests__/config-merge-shared.test.ts
@@ -0,0 +1,99 @@
+// @vitest-environment node
+import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest';
+import { mkdtemp, rm } from 'node:fs/promises';
+import { tmpdir } from 'node:os';
+import path from 'node:path';
+import { NextRequest } from 'next/server';
+
+// Some admin saves change one entry of a list: the per-domain branding, the
+// client secrets of the JMAP servers. Built on this instance's copy of the
+// list, they dropped what another instance (or a parallel upload here) had
+// saved a moment before (#1066).
+
+vi.mock('@/lib/admin/session', () => ({
+  requireAdminAuth: async () => ({ payload: { role: 'admin' } }),
+  getClientIP: () => '127.0.0.1',
+}));
+vi.mock('@/lib/admin/audit', () => ({ auditLog: async () => {} }));
+
+import { POST as uploadBranding, DELETE as deleteBranding } from '../branding/route';
+import { PATCH as patchConfig } from '../config/route';
+import { configManager } from '@/lib/admin/config-manager';
+import { adminConfigDocs } from '@/lib/admin/admin-store';
+import { setStoreForTests } from '@/lib/shared-store';
+import { resetLocalStoreForTests } from '@/lib/shared-store/local';
+import { INIT_EPOCH, markEpochsSeen, resetChangesForTests } from '@/lib/shared-store/changes';
+import { separateFakeStore } from '@/lib/admin/__tests__/shared-store-fake';
+
+let dir: string;
+const stored = async () => JSON.parse((await adminConfigDocs().get('config.json'))!.data.toString('utf-8'));
+/** Another instance saved this; its notice hasn't arrived here yet. */
+const savedElsewhere = (config: Record<string, unknown>) => adminConfigDocs().put('config.json', JSON.stringify(config));
+
+function upload(host: string) {
+  const form = new FormData();
+  form.set('file', new File([new Uint8Array([0x89, 0x50, 0x4e, 0x47])], 'logo.png', { type: 'image/png' }));
+  form.set('slot', 'faviconUrl');
+  form.set('host', host);
+  return uploadBranding(new NextRequest('https://mail.example/api/admin/branding', { method: 'POST', body: form }));
+}
+
+beforeEach(async () => {
+  dir = await mkdtemp(path.join(tmpdir(), 'bw-config-merge-'));
+  vi.stubEnv('ADMIN_CONFIG_DIR', path.join(dir, 'config'));
+  vi.stubEnv('ADMIN_STATE_DIR', path.join(dir, 'state'));
+  resetLocalStoreForTests();
+  resetChangesForTests();
+  const store = separateFakeStore(path.join(dir, 'store'));
+  setStoreForTests(store);
+  await store.epochs.bump(INIT_EPOCH);
+  await savedElsewhere({ setupComplete: true });
+  await markEpochsSeen();
+  await configManager.load();
+});
+
+afterEach(async () => {
+  setStoreForTests(null);
+  resetChangesForTests();
+  resetLocalStoreForTests();
+  vi.unstubAllEnvs();
+  await rm(dir, { recursive: true, force: true });
+});
+
+describe('list saves with a shared store', () => {
+  it('keeps another instance\'s domain branding when uploading for another domain', async () => {
+    await savedElsewhere({ setupComplete: true, domainBranding: [{ host: 'a.example', faviconUrl: '/api/admin/branding/a.png' }] });
+    expect((await upload('b.example')).status).toBe(200);
+    const hosts = (await stored()).domainBranding.map((e: { host: string }) => e.host).sort();
+    expect(hosts).toEqual(['a.example', 'b.example']);
+
+    await savedElsewhere({ ...(await stored()), domainBranding: [...(await stored()).domainBranding, { host: 'c.example', faviconUrl: '/x.png' }] });
+    const res = await deleteBranding(new NextRequest('https://mail.example/api/admin/branding', {
+      method: 'DELETE',
+      body: JSON.stringify({ slot: 'faviconUrl', host: 'b.example' }),
+    }));
+    expect(res.status).toBe(200);
+    expect((await stored()).domainBranding.map((e: { host: string }) => e.host)).toContain('c.example');
+  });
+
+  it('keeps both of two uploads for different domains at once', async () => {
+    const results = await Promise.all([upload('a.example'), upload('b.example')]);
+    expect(results.map((r) => r.status)).toEqual([200, 200]);
+    expect((await stored()).domainBranding.map((e: { host: string }) => e.host).sort()).toEqual(['a.example', 'b.example']);
+  });
+
+  it('keeps a JMAP server\'s client secret another instance just saved', async () => {
+    const server = { id: 'corp', label: 'Corp', url: 'https://mail.corp.example', oauth: { clientId: 'webmail' } };
+    await savedElsewhere({ setupComplete: true, jmapServers: [{ ...server, oauth: { clientId: 'webmail', clientSecret: 'secret-saved-elsewhere' } }] });
+    // The dashboard never has the secret, so it sends the entry without it.
+    const res = await patchConfig(new NextRequest('https://mail.example/api/admin/config', {
+      method: 'PATCH',
+      headers: { 'content-type': 'application/json' },
+      body: JSON.stringify({ jmapServers: [{ ...server, label: 'Corp mail' }], appName: 'Renamed' }),
+    }));
+    expect(res.status).toBe(200);
+    const config = await stored();
+    expect(config.appName).toBe('Renamed');
+    expect(config.jmapServers[0]).toMatchObject({ label: 'Corp mail', oauth: { clientId: 'webmail', clientSecret: 'secret-saved-elsewhere' } });
+  });
+});
diff --git a/app/api/admin/branding/route.ts b/app/api/admin/branding/route.ts
index b7d5e4ff5..14c0864d2 100644
--- a/app/api/admin/branding/route.ts
+++ b/app/api/admin/branding/route.ts
@@ -193,9 +193,10 @@ export async function POST(request: NextRequest) {
     await configManager.ensureLoaded();
 
     if (host) {
-      const current = parseDomainBranding(configManager.get<unknown>('domainBranding', []));
-      const next = mergeDomainEntry(current, host, { [slot]: servedUrl });
-      await configManager.setAdminConfig({ domainBranding: next });
+      // Built on the stored list, so a save of another domain at the same
+      // time (here or on another instance) stays.
+      await configManager.updateAdminConfig<unknown>('domainBranding', (current) =>
+        mergeDomainEntry(parseDomainBranding(current), host, { [slot]: servedUrl }), []);
     } else {
       await configManager.setAdminConfig({ [slot]: servedUrl });
     }
@@ -269,9 +270,8 @@ export async function DELETE(request: NextRequest) {
 
     await configManager.ensureLoaded();
     if (host) {
-      const current = parseDomainBranding(configManager.get<unknown>('domainBranding', []));
-      const next = clearDomainKeys(current, host, [slot as BrandingOverrideKey]);
-      await configManager.setAdminConfig({ domainBranding: next });
+      await configManager.updateAdminConfig<unknown>('domainBranding', (current) =>
+        clearDomainKeys(parseDomainBranding(current), host, [slot as BrandingOverrideKey]), []);
     } else {
       await configManager.removeAdminOverride(slot);
     }
diff --git a/app/api/admin/config/route.ts b/app/api/admin/config/route.ts
index 33e3cd203..dd223fafd 100644
--- a/app/api/admin/config/route.ts
+++ b/app/api/admin/config/route.ts
@@ -135,6 +135,7 @@ export async function PATCH(request: NextRequest) {
 
     // Normalize jmapServers: pass through the parser so invalid entries are
     // rejected (bad ids, duplicate ids, non-HTTP URLs) before they're persisted.
+    let jmapServers: unknown[] | null = null;
     if ('jmapServers' in updates) {
       const incoming = updates.jmapServers;
       if (incoming != null && !Array.isArray(incoming)) {
@@ -151,6 +152,8 @@ export async function PATCH(request: NextRequest) {
           error: 'One or more jmapServers entries are invalid (each needs a unique id, label, and HTTP(S) url).',
         }, { status: 400 });
       }
+      // Saved on its own below, with the secrets of the stored list.
+      jmapServers = Array.isArray(incoming) ? incoming : [];
       updates.jmapServers = sanitized;
     }
 
@@ -179,7 +182,18 @@ export async function PATCH(request: NextRequest) {
       oldValues[key] = configManager.get(key);
     }
 
-    await configManager.setAdminConfig(updates);
+    if (jmapServers) {
+      // The secrets the dashboard didn't send come from the stored list, not
+      // this instance's copy: a secret saved elsewhere a moment ago stays.
+      const { jmapServers: _servers, ...rest } = updates;
+      void _servers;
+      if (Object.keys(rest).length > 0) await configManager.setAdminConfig(rest);
+      const incoming = jmapServers;
+      updates.jmapServers = await configManager.updateAdminConfig<unknown>('jmapServers', (current) =>
+        parseJmapServers(withStoredClientSecrets(incoming, parseJmapServers(current))), []);
+    } else {
+      await configManager.setAdminConfig(updates);
+    }
     await auditLog('config.update', { changes: Object.keys(updates).map(k => ({ key: k, old: oldValues[k], new: updates[k] })) }, ip);
 
     return NextResponse.json({ ok: true });