Backing up the file/folder structure on a DFS share doesn’t work, and backing up DFS through the shadow copy components is painfully slow, so I directly backup the DFS share. The DFS configuration is backed up when I backup my domain controllers. The configuration and the data are all I’m concerned with backing up, so half of that problem is already solved for me. I back up my data by creating my selection list at the share level instead of at the file structure/folder level and exclude the DFSRPrivate folders in each share, as they won’t backup anyway.

Fizxed with thanks to http://www.backupexecfaq.com/articles/real-world/backing-up-dfs-data.html