You can try to replace the existing server configuration. You can do it in the following way.
1. Add a your new TFS server but do not change anything to your projects or delete the old server connection
2. In the database replace the Settings field of the old server with the new one and delete the new one
SET Settings = (SELECT TOP 1 Settings FROM SynchronizationServer WHERE SynchronizationServerID = [last one])
WHERE SynchronizationServerID = [oldone]
If this doesn't help you can create new project and do full project sync.