This can happen when you convert a physical server to a virtual server.
Event Type: Error
Event Source: NtFrs
Event Category: None
Event ID: 13559
The File Replication Service has detected that the replica root path has changed from “c:\windows\sysvol\domain” to “c:\windows\sysvol\domain”. If this is an intentional move then a file with the name NTFRS_CMD_FILE_MOVE_ROOT needs to be created under the new root path.
This was detected for the following replica set:
“DOMAIN SYSTEM VOLUME (SYSVOL SHARE)”
Changing the replica root path is a two step process which is triggered by the creation of the NTFRS_CMD_FILE_MOVE_ROOT file.
 At the first poll which will occur in 60 minutes this computer will be deleted from the replica set.
 At the poll following the deletion this computer will be re-added to the replica set with the new root path. This re-addition will trigger a full tree sync for the replica set. At the end of the sync all the files will be at the new location. The files may or may not be deleted from the old location depending on whether they are needed or not.
For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.
The solution to the problem is to create a file in the c:\windows\sysvol\domain” named NTFRS_CMD_FILE_MOVE_ROOT with out any file extension, then restart the
file replication service. Wait a couple of minutes and check your event’s in the File Replication service and you see that everything is working for you.