When using Server Migration Tool, it will duplicate entire settings/configuration/GUIDs. It’s okay to use when importing to a new server as long as the old server will be disconnected.
However, if you want to keep both servers alive (i.e. mirror on-premise domain structure to SaaS environment), it would cause some issues.
To resolve the issue:
- When executing Server Migration Tool, add a parameter to refresh GUIDs:
> ServerMigrationTool.exe GenDomainGuid
- Use the exported file to import it, so that the new server will have the same domain structure without issues.
This is applicable not just for On-Premise-to-SaaS migration, but also for On-Premise-to-On-Premise environments.