This is actually covered in Microsoft's FAQ for DFS. The answer is, it depends. Mostly yes but not recommended if using replication. DFS-R is made for replicating mostly static files. Users' documents change a lot and DFS-R may not be efficient at replicating the changes.
There are two levels of permissions when accessing network file resources:
When you access local data, file access is controlled by only the NTFS permissions. But when you access a file share over the network, access is controlled by the combination of the NTFS permissions AND the share permissions. The effective permissions are the most restrictive of the two. Older OS's (like 2003) defaulted to share perms of Everyone/Full, but newer OS's (2008 or later) default to share perms of Everyone/Read. Suspect you have defaults in place (that you may have been unaware of) at the share perms level. http://technet.microsoft.com/en-us/library/cc754178.aspx
In most cases, I prefer to change the share perms to Everyone/Full or Change, which means I only have to worry about managing permissions at the NTFS level.
If this is not the case, could you please describe the NTFS perms, and share perms in place on each DFS target.
This is an old thread but maybe someone could benefit from my comment.
There is a service called Distributed Link Tracking Client that finds a file that was moved or renamed on an NTFS network share (KB312403). This works for shell shortcuts and OLE links as well.
We had a similar problem when we moved folders on our DFS share. The experience was that after the folders were moved the shortcuts on users' desktops were changed from \dfsvirtualname\sharename to \realservername\sharename. Yes, the files were found but only one time. The next time the folder was moved (like archived to a folder named 2014, etc) the shortcuts broke.
The issue you have with some files could be that those files were already moved in the past and the Distributed Link Tracking Client found them, changing the
link to a full \realservername\sharename reference and now it can't find the moved file.
Best Answer
This is actually covered in Microsoft's FAQ for DFS. The answer is, it depends. Mostly yes but not recommended if using replication. DFS-R is made for replicating mostly static files. Users' documents change a lot and DFS-R may not be efficient at replicating the changes.
http://www.microsoft.com/windowsserversystem/dfs/dfsfaq.mspx#EWKAC See the question, "Can I use DFS with Offline Files and redirected My Documents folders?"