For whatever reason (infrastructure upgrade plan for instance), you may need to replace the server with Azure AD Connect tool installed to a new one.
To succeed with server replacement, Azure AD Connect tool must be migrated following the correct steps to avoid potential synchronization issues.
Migrate Azure AD Connect to the new server
The migration process is pretty quick and during the procedure changes between directories won't be synchronized.
Enable Staging Mode in the OLD server
From the old server run the AAD Connect tool and select Configure.
Select Configure staging mode and click Next.
Login to your Office 365 portal, and check the synchronization status.
The new server is now fully operative and the old server can be safely removed from the domain and dismissed.
Read the full article on StarWind blog.