Fix: Warning When Configuring New Domain Controller Settings in Azure AD Connect Synchronization Service Manager
This article explains why this warning occurs and how to safely proceed with updating Domain Controller settings.
🔍 The Symptoms / Error Message
⚠️ Warning Encountered
When navigating to Connector Properties → Configure Directory Partitions, the following message appears:
“This management agent was created using a wizard. Changing the configuration outside of the wizard is not recommended.”
🧠 Root Cause
💡 Why This Happens
- The configuration was originally created using the Azure AD Connect wizard
- Synchronization Service Manager (miisclient.exe) is considered an advanced tool
- Any changes made outside the wizard trigger a standard advisory warning
✅ Important
This is an informational warning only and does not indicate a failure. It is completely safe to proceed when making controlled, intentional configuration changes.
🛠️ Step-by-Step Resolution
Proceed with the Warning
The warning is advisory — it does not block configuration changes or indicate a problem.
📋 Steps
- Click OK on the warning message
- This allows access to the advanced configuration settings
Open Domain Controller Settings
Navigate to the Active Directory Connector properties in Synchronization Service Manager.
📋 Steps
- Open Synchronization Service Manager
- Go to Connectors
- Select the Active Directory Connector
- Click Properties
- Navigate to Configure Directory Partitions
- Click Configure under Domain controller connection settings
Update Domain Controller Configuration
The next steps depend on whether preferred Domain Controllers are already configured.
✅ If “Only use preferred domain controllers” is Enabled
- Remove the old Domain Controller from the list
- Add the new Domain Controller in FQDN format — e.g.
NewDC.domain.local - Move the new DC to the top of the list
- Click OK to save the configuration
✅ If “Only use preferred domain controllers” is Disabled
- Azure AD Connect automatically discovers Domain Controllers using DNS and Active Directory site topology
- No manual configuration is required — the system will automatically start using the new DC
Verify Domain Controller Usage (PowerShell)
Run on the Azure AD Connect server to confirm which Domain Controller was last used.
Import-Module ADSync ((Get-ADSyncConnector).Partitions.Parameters | Where-Object {$_.Name -eq 'last-dc'}).Value
✅ Expected Output
Displays the FQDN of the last Domain Controller used by Azure AD Connect — confirm it reflects the new DC after configuration.
Trigger Synchronisation (PowerShell)
Run a delta sync cycle to apply the new Domain Controller configuration immediately.
Import-Module ADSync Start-ADSyncSyncCycle -PolicyType Delta
Validate Synchronisation
Confirm the sync cycle completed successfully after the Domain Controller change.
✅ Verification Checklist
- Open Synchronization Service Manager
- Verify Import completed successfully
- Verify Synchronization completed successfully
- Confirm no connector errors are present
Validate Domain Controller Health
Before decommissioning any Domain Controller, verify AD replication is healthy across all controllers.
repadmin /replsummary
✅ Expected Outcome
All Domain Controllers should show healthy replication status with no failures before the old DC is decommissioned.
💡 Best Practices & Recommendations
- Use preferred Domain Controller settings only when required — for example, when network constraints or site topology require a specific DC
- Always verify AD replication health with repadmin /replsummary before removing or decommissioning any Domain Controller
- Rely on automatic DC discovery unless a specific business or network requirement exists
📚 References & Further Reading
- 🔗 What is Hybrid Identity — Microsoft Learn
- 🔗 Troubleshoot Azure AD Connect Sync Errors — Microsoft Learn
- 🔗 Active Directory Replication Concepts — Microsoft Learn
✅ Final Takeaway
The warning shown in Synchronization Service Manager is expected and safe to proceed through when making controlled configuration changes.
Update Domain Controller settings as needed, verify the active DC using PowerShell, and confirm successful synchronisation before making any infrastructure changes.