Jose Barreto's Blog Post Covers The Basics:
If you have an environment transitioning from 2003 to 2008. Once your domain controllers are all 2008 and you can use the proper domain and forest levels, rather than trying to convert a smaller 2000 DFS configuration I would consider starting DFS over with the following steps:
-document thoroughly your configuration.
-review what you have and what you don't need. (how many namespace servers are you using?)
-backup the data on both the primary and replica location
-log off users to make sure the data is not in use
-delete your old namespaces, namespace servers, and replications. (not the data!)
-recreate DFS using 2008 only namespace servers to rebuild your DFS paths
-carefully recreate your DFS replicas
-restart servers and desktops as necessary
Note: Just because you are referencing data on a server or system does NOT mean it needs to be a Nameserver. Think of Nameservers as DNS servers pointing you to the data not necessarily hosts of the data.