First published on TECHNET on Dec 28, 2005
On several occasions we've seen customers enable DFS Replication on the root of a volume, such as C:. Although DFS Replication supports configuring a volume root as the local path of a replicated folder, we don’t recommend this configuration for the following reasons:
DFS Replication replicates metadata (including ACLs and attributes) that are set on the local path of the replicated folder. Volume roots are special because they always implicitly have both the hidden and system attribute bits set. If replication partners are configured to have the corresponding local path of the replicated folder to be some place other than a volume root, that replicated folder will have system and hidden attributes set.
System folders are typically placed in the volume root. DFS Replication is designed to ignore these folders, but there might be interoperability issues with third-party applications.