Will upgrading my DFS Namespace affect my replication groups associated with that Namepsace?

Hello community! I'm looking to upgrade my DFS Namespace from Windows 2000 mode to 2008 mode. I have two sites each using DFS replication with one server at each site. I've just replaced a server at site A, but I named the server too long for NetBIOS and now DFS referrals for the namespace aren't perfect. I'd like it to use DNS with a suffix (FQDN) but am afraid if I remove the namespace and re-add it, it will re-replicate my groups. This cannot happen! Any assurance is appreciated. Thanks everybody!