Today, i did my first ever gig migrating a Windows 2000 AD based DFS with FRS environment into a 2003 R2 DFS-R environment (should also be the same for a 2008/2008 R2 DFS environment). These ofcourse should be few and far between, because, well, if your still running 2000 and dont have a good reason (such as a contract with the federal government that stipulates you will deliver on win2000) – you have issues and shouldnt be spending time reading blogs.
Anyhoo, i found this method effective for moving a domain based root and its sub-folders across:
1) Leave the existing DFS namespaces intact
2) Add the new folder targets to the namespaces, but ensure that FRS replication is disabled (do this via the windows 2000 DFS admin tool), and referrals are disabled (for the time being)
3) Create the new folder structure on your hub (if your using hub and spoke)
4) Create your replication groups, schedules etc and allow appropriate time to replicate
5) After replication has completed, enable referrals for the now populated folder targets
6) Remove your old-school windows 2000 targets