I've ready that you can and initial synchronization will take off again, but I've also heard that you should.
We have two 2008 R2 file servers that use DFS to replicate both ways. One server has been having issues and I decided it is time to replace it. I built a new 2012 R2 server and pre-seeded it's 5 disks over the weekend using robocopy and had no problems.
It wasn't until I had began initial replication that I discovered that on one disk, a couple folders deep, all of the permissions were incorrect. They had the permissions of the root folder (hundreds, maybe thousands of folders).
I deleted the servers membership from the replication group, received the event letting me know that it had stopped and was able to correct the security using 'robocopy <source> <destination> /secfix /copy:atsou /e /xx' That copied only the NTFS permissions over and no data.
I need to put it back as a member of the replication group and begin initial replication, but I've been reading that if I do so, the files I preseeded yesterday could replicate over the files on the other file servers, possibly overwriting work done today.
Anyone have ideas?