diff --git a/src/commands/config.ts b/src/commands/config.ts
index 4a3382b95..90537f00a 100644
--- a/src/commands/config.ts
+++ b/src/commands/config.ts
@@ -539,6 +539,7 @@ export function registerConfigCommand(program: Command): void {
           delivery: currentState.delivery,
           workflows: [...currentState.workflows],
         };
+        let workflowSelectionChanged = false;
 
         if (action === 'both' || action === 'delivery') {
           const deliveryChoices: { value: Delivery; name: string; description: string }[] = [
@@ -599,7 +600,12 @@ export function registerConfigCommand(program: Command): void {
             choices: ALL_WORKFLOWS.map(formatWorkflowChoice),
           });
           nextState.workflows = selectedWorkflows;
-          nextState.profile = deriveProfileFromWorkflowSelection(selectedWorkflows);
+          workflowSelectionChanged =
+            selectedWorkflows.length !== currentState.workflows.length ||
+            selectedWorkflows.some((workflow) => !currentState.workflows.includes(workflow));
+          nextState.profile = workflowSelectionChanged
+            ? deriveProfileFromWorkflowSelection(selectedWorkflows)
+            : currentState.profile;
         }
 
         const diff = diffProfileState(currentState, nextState);
@@ -617,7 +623,9 @@ export function registerConfigCommand(program: Command): void {
 
         config.profile = nextState.profile;
         config.delivery = nextState.delivery;
-        config.workflows = nextState.workflows;
+        if (currentState.profile !== 'custom' || workflowSelectionChanged) {
+          config.workflows = nextState.workflows;
+        }
         saveGlobalConfig(config);
 
         // Check if inside an OpenSpec project
diff --git a/src/core/profiles.ts b/src/core/profiles.ts
index acdc3ec95..64351cb8a 100644
--- a/src/core/profiles.ts
+++ b/src/core/profiles.ts
@@ -38,14 +38,27 @@ export type CoreWorkflowId = (typeof CORE_WORKFLOWS)[number];
  * Resolves which workflows should be active for a given profile configuration.
  *
  * - 'core' profile always returns CORE_WORKFLOWS
- * - 'custom' profile returns the provided customWorkflows, or empty array if not provided
+ * - 'custom' profile returns the provided customWorkflows and required dependencies
  */
 export function getProfileWorkflows(
   profile: Profile,
   customWorkflows?: string[]
 ): readonly string[] {
   if (profile === 'custom') {
-    return customWorkflows ?? [];
+    const workflows = customWorkflows ?? [];
+    const syncDependentIndex = workflows.findIndex(
+      (workflow) => workflow === 'archive' || workflow === 'bulk-archive'
+    );
+
+    if (syncDependentIndex !== -1 && !workflows.includes('sync')) {
+      return [
+        ...workflows.slice(0, syncDependentIndex),
+        'sync',
+        ...workflows.slice(syncDependentIndex),
+      ];
+    }
+
+    return workflows;
   }
   return CORE_WORKFLOWS;
 }
diff --git a/src/core/update.ts b/src/core/update.ts
index 69fa4bafe..4c74d0851 100644
--- a/src/core/update.ts
+++ b/src/core/update.ts
@@ -247,7 +247,7 @@ export class UpdateCommand {
       // Still check for new tool directories and extra workflows
       this.detectNewTools(resolvedProjectPath, configuredTools);
       this.displayExtraWorkflowsNote(resolvedProjectPath, configuredTools, desiredWorkflows);
-      this.displayMissingCoreWorkflowsNote(profile, globalConfig.workflows);
+      this.displayMissingCoreWorkflowsNote(profile, desiredWorkflows);
       this.displaySetupNotes(configuredTools);
       return;
     }
@@ -474,7 +474,7 @@ export class UpdateCommand {
 
     // 14. Display note about extra workflows not in profile
     this.displayExtraWorkflowsNote(resolvedProjectPath, configuredAndNewTools, desiredWorkflows);
-    this.displayMissingCoreWorkflowsNote(profile, globalConfig.workflows);
+    this.displayMissingCoreWorkflowsNote(profile, desiredWorkflows);
     this.displaySetupNotes(configuredAndNewTools);
 
     // 15. List affected tools
@@ -1100,7 +1100,12 @@ export class UpdateCommand {
       }
     }
 
-    const inferredCodexWorkflows = getLegacyWorkflowIdsForTool(detection, 'codex');
+    const inferredCodexWorkflows = getProfileWorkflows(
+      'custom',
+      getLegacyWorkflowIdsForTool(detection, 'codex')
+    ).filter((workflow): workflow is (typeof ALL_WORKFLOWS)[number] =>
+      (ALL_WORKFLOWS as readonly string[]).includes(workflow)
+    );
 
     // Create skills/commands for selected tools using effective profile+delivery.
     const newlyConfigured: string[] = [];
diff --git a/test/commands/config-profile.test.ts b/test/commands/config-profile.test.ts
index bb130a8f6..3137814e6 100644
--- a/test/commands/config-profile.test.ts
+++ b/test/commands/config-profile.test.ts
@@ -288,6 +288,65 @@ describe('config profile interactive flow', () => {
     expect(consoleLogSpy).toHaveBeenCalledWith('No config changes.');
   });
 
+  it('should preserve a custom profile when dependency expansion matches the core set', async () => {
+    const { saveGlobalConfig, getGlobalConfig, getGlobalConfigPath } = await import('../../src/core/global-config.js');
+    const { select, checkbox, confirm } = await getPromptMocks();
+
+    saveGlobalConfig({
+      featureFlags: {},
+      profile: 'custom',
+      delivery: 'both',
+      workflows: ['propose', 'explore', 'apply', 'update', 'archive'],
+    });
+    const configPath = getGlobalConfigPath();
+    const beforeContent = fs.readFileSync(configPath, 'utf-8');
+
+    select.mockResolvedValueOnce('workflows');
+    checkbox.mockResolvedValueOnce(['propose', 'explore', 'apply', 'update', 'sync', 'archive']);
+
+    await runConfigCommand(['profile']);
+
+    expect(getGlobalConfig().profile).toBe('custom');
+    expect(fs.readFileSync(configPath, 'utf-8')).toBe(beforeContent);
+    expect(confirm).not.toHaveBeenCalled();
+    expect(consoleLogSpy).toHaveBeenCalledWith('No config changes.');
+  });
+
+  it.each(['delivery', 'both'] as const)(
+    'should preserve raw custom workflows during a %s change',
+    async (action) => {
+      const { saveGlobalConfig, getGlobalConfig } = await import('../../src/core/global-config.js');
+      const { select, checkbox } = await getPromptMocks();
+
+      saveGlobalConfig({
+        featureFlags: {},
+        profile: 'custom',
+        delivery: 'both',
+        workflows: ['propose', 'explore', 'apply', 'update', 'archive'],
+      });
+      select.mockResolvedValueOnce(action);
+      select.mockResolvedValueOnce('skills');
+      if (action === 'both') {
+        checkbox.mockResolvedValueOnce([
+          'propose',
+          'explore',
+          'apply',
+          'update',
+          'sync',
+          'archive',
+        ]);
+      }
+
+      await runConfigCommand(['profile']);
+
+      expect(getGlobalConfig()).toMatchObject({
+        profile: 'custom',
+        delivery: 'skills',
+        workflows: ['propose', 'explore', 'apply', 'update', 'archive'],
+      });
+    }
+  );
+
   it('keep action should warn when project files drift from global config', async () => {
     const { saveGlobalConfig } = await import('../../src/core/global-config.js');
     const { select } = await getPromptMocks();
diff --git a/test/core/init.test.ts b/test/core/init.test.ts
index 42a60a79f..388c19917 100644
--- a/test/core/init.test.ts
+++ b/test/core/init.test.ts
@@ -118,6 +118,34 @@ describe('InitCommand', () => {
       }
     });
 
+    it.each([
+      ['archive', 'openspec-archive-change'],
+      ['bulk-archive', 'openspec-bulk-archive-change'],
+    ] as const)(
+      'should install the sync workflow required by %s in a custom profile',
+      async (archiveWorkflow, archiveSkill) => {
+        saveGlobalConfig({
+          featureFlags: {},
+          profile: 'custom',
+          delivery: 'both',
+          workflows: ['propose', 'explore', 'apply', archiveWorkflow],
+        });
+
+        const initCommand = new InitCommand({ tools: 'claude', force: true });
+        await initCommand.execute(testDir);
+
+        await expect(
+          fs.access(path.join(testDir, '.claude', 'skills', archiveSkill, 'SKILL.md'))
+        ).resolves.toBeUndefined();
+        await expect(
+          fs.access(path.join(testDir, '.claude', 'skills', 'openspec-sync-specs', 'SKILL.md'))
+        ).resolves.toBeUndefined();
+        await expect(
+          fs.access(path.join(testDir, '.claude', 'commands', 'opsx', 'sync.md'))
+        ).resolves.toBeUndefined();
+      }
+    );
+
     it('should create core profile commands for Claude Code by default', async () => {
       const initCommand = new InitCommand({ tools: 'claude', force: true });
 
diff --git a/test/core/profiles.test.ts b/test/core/profiles.test.ts
index b06456e01..79ff45a1c 100644
--- a/test/core/profiles.test.ts
+++ b/test/core/profiles.test.ts
@@ -54,6 +54,32 @@ describe('profiles', () => {
       expect(result).toEqual(customWorkflows);
     });
 
+    it('should include sync when a custom profile selects archive', () => {
+      const result = getProfileWorkflows('custom', ['propose', 'explore', 'apply', 'archive']);
+      expect(result).toEqual(['propose', 'explore', 'apply', 'sync', 'archive']);
+    });
+
+    it('should include sync when a custom profile selects bulk archive', () => {
+      const result = getProfileWorkflows('custom', ['explore', 'bulk-archive']);
+      expect(result).toEqual(['explore', 'sync', 'bulk-archive']);
+    });
+
+    it('should not duplicate or reorder an existing sync dependency', () => {
+      const workflows = ['sync', 'archive', 'bulk-archive'];
+      const result = getProfileWorkflows('custom', workflows);
+
+      expect(result).toEqual(workflows);
+      expect(result).toBe(workflows);
+    });
+
+    it('should not mutate the custom workflow selection when adding sync', () => {
+      const workflows = ['archive', 'bulk-archive'];
+      const result = getProfileWorkflows('custom', workflows);
+
+      expect(result).toEqual(['sync', 'archive', 'bulk-archive']);
+      expect(workflows).toEqual(['archive', 'bulk-archive']);
+    });
+
     it('should return empty array for custom profile with no customWorkflows', () => {
       const result = getProfileWorkflows('custom');
       expect(result).toEqual([]);
diff --git a/test/core/update.test.ts b/test/core/update.test.ts
index b541bdadc..c3085e878 100644
--- a/test/core/update.test.ts
+++ b/test/core/update.test.ts
@@ -2333,6 +2333,33 @@ ${OPENSPEC_MARKERS.end}
       )).toBe(false);
     });
 
+    it.each([
+      ['opsx-archive.md', 'openspec-archive-change'],
+      ['opsx-bulk-archive.md', 'openspec-bulk-archive-change'],
+    ])('should include sync when replacing legacy Codex %s', async (promptName, archiveSkill) => {
+      setMockConfig({
+        featureFlags: {},
+        profile: 'core',
+        delivery: 'skills',
+      });
+
+      const promptDir = path.join(process.env.CODEX_HOME!, 'prompts');
+      const managedPrompt = path.join(promptDir, promptName);
+      await fs.mkdir(promptDir, { recursive: true });
+      await fs.writeFile(managedPrompt, 'legacy archive prompt');
+
+      const forceUpdateCommand = new UpdateCommand({ force: true });
+      await forceUpdateCommand.execute(testDir);
+
+      expect(await FileSystemUtils.fileExists(managedPrompt)).toBe(false);
+      expect(await FileSystemUtils.fileExists(
+        path.join(testDir, '.agents', 'skills', archiveSkill, 'SKILL.md')
+      )).toBe(true);
+      expect(await FileSystemUtils.fileExists(
+        path.join(testDir, '.agents', 'skills', 'openspec-sync-specs', 'SKILL.md')
+      )).toBe(true);
+    });
+
     it('should print a skill-based getting-started menu when a legacy upgrade newly configures codex', async () => {
       setMockConfig({
         featureFlags: {},
@@ -3003,40 +3030,63 @@ More user content after markers.
       )).toBe(false);
     });
 
-    it('should list missing core workflows when custom profile preserves the old core workflow set', async () => {
-      setMockConfig({
-        featureFlags: {},
-        profile: 'custom',
-        delivery: 'both',
-        workflows: ['propose', 'explore', 'apply', 'archive'],
-      });
-
-      const initCommand = new InitCommand({ tools: 'claude', force: true });
-      await initCommand.execute(testDir);
-
-      const consoleSpy = vi.spyOn(console, 'log');
+    it.each(['skills', 'commands', 'both'] as const)(
+      'should repair an archive profile missing sync with %s delivery',
+      async (delivery) => {
+        setMockConfig({
+          featureFlags: {},
+          profile: 'custom',
+          delivery,
+          workflows: ['propose', 'explore', 'apply', 'archive'],
+        });
 
-      await updateCommand.execute(testDir);
+        const archiveSkill = path.join(
+          testDir,
+          '.claude',
+          'skills',
+          'openspec-archive-change',
+          'SKILL.md'
+        );
+        const archiveCommand = path.join(
+          testDir,
+          '.claude',
+          'commands',
+          'opsx',
+          'archive.md'
+        );
+        if (delivery !== 'commands') {
+          await fs.mkdir(path.dirname(archiveSkill), { recursive: true });
+          await fs.writeFile(archiveSkill, 'old archive skill');
+        }
+        if (delivery !== 'skills') {
+          await fs.mkdir(path.dirname(archiveCommand), { recursive: true });
+          await fs.writeFile(archiveCommand, 'old archive command');
+        }
 
-      const calls = consoleSpy.mock.calls.map(call =>
-        call.map(arg => String(arg)).join(' ')
-      );
-      expect(calls.some(call =>
-        call.includes('Your custom profile is missing 2 core workflows: update, sync')
-      )).toBe(true);
-      expect(calls.some(call =>
-        call.includes('openspec config profile core')
-      )).toBe(true);
+        const consoleSpy = vi.spyOn(console, 'log');
 
-      expect(await FileSystemUtils.fileExists(
-        path.join(testDir, '.claude', 'skills', 'openspec-sync-specs', 'SKILL.md')
-      )).toBe(false);
-      expect(await FileSystemUtils.fileExists(
-        path.join(testDir, '.claude', 'commands', 'opsx', 'sync.md')
-      )).toBe(false);
+        await updateCommand.execute(testDir);
 
-      consoleSpy.mockRestore();
-    });
+        const calls = consoleSpy.mock.calls.map(call =>
+          call.map(arg => String(arg)).join(' ')
+        );
+        expect(calls.some(call =>
+          call.includes('Your custom profile is missing 1 core workflow: update')
+        )).toBe(true);
+        expect(calls.some(call =>
+          call.includes('openspec config profile core')
+        )).toBe(true);
+
+        expect(await FileSystemUtils.fileExists(
+          path.join(testDir, '.claude', 'skills', 'openspec-sync-specs', 'SKILL.md')
+        )).toBe(delivery !== 'commands');
+        expect(await FileSystemUtils.fileExists(
+          path.join(testDir, '.claude', 'commands', 'opsx', 'sync.md')
+        )).toBe(delivery !== 'skills');
+
+        consoleSpy.mockRestore();
+      }
+    );
 
     it('should list a single missing core workflow when custom profile lacks only update', async () => {
       setMockConfig({