I have a SBS 2011 box that was migrated from 2003 about one year ago. About a week ago, Event ID 13559 appeared in the File Replication Service event viewer. Up until then it was all 13501 & 13516's which would be indications that things are going well. Here is the Event 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 5 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.
Nothing was moved on this server, nor was anything virtualized as I've seen as the culprit on other articles. Disk space is fine, and this event just appeared in the middle of the day, approx. 12:02 PM local time.
I'm very reluctant to follow the Event's suggested fix as there are no other DC's to replicate from. SBS 2011 is the only one on the network. I've seen other suggestions about restarting NTFRS but am very reluctant.
Any help would be greatly appreciated.