We have DFS setup using the DFS Management Administrator Tool. I turned on replication in the Distributed File System Administrator Tool as well and this morning we lost tons of files from that share. Please explain to me why this was wrong and if there is anything that can be done to repair it. (No, we don't have backups. We have some shadow copies, but those were deleted as well. We have been using DFS as its own backup)
Before I say anything else,
DFSR is not a backup! Don't use it this way, or you'll get burned again eventually.
So for clarification, you had Server1 with a set of files, and Server2 without that set of files. You added a folder target on Server2, and then created a replication group between the two servers?
In theory if it was done as above then Server2 would have been in an initial replication state, received the files from Server1, and then made active.
Most likely what happened is Server2 was taken as authoritative during the replication group setup, which wiped out the share on Server1.
I would check the DFSR event log on both servers, looking for this event:
This event will describe which files were removed, and where they now exist. Your conflict and deleted folder is typically with the DFS share, in a hidden folder named DFSRPrivate. Note: By default this folder will only hold 660MB of files, and then rotate that space afterwards.
Also check the Pre-Existing folder within the DFSRPrivate folder, as your files may be there too.