HELP! - DFS Problems

I really hope someone can help me out with this. We have two DCs which replicate certain folders. Today I noticed this had not been replicating so I went in and stopped then reconfigured the replication for these folders. Now all replicated folders have a folder called DO_NOT_REMOVE_NtFrs_PreInstall_Directory and NtFrs_PreExisting__See_EventLog. The folder that starts with NtFrs contains all the original files and folders. I have a major problem here because none of the profiles can be found because they have all been moved to this NtFrs folder. Does anyone know what this means? Can anyone please help me? Our main DC still has all the original information.