Oy... so i've gone through this before and it's not the most fun. Basically, you need to go offline for each client computer. Then copy the offline files to a safe location, and finally purge the offline folder cache (follow the instuctions linked here http://support.microsoft.com/kb/230738). Then you can copy the file back and everything should be in sync.
Your other option is to create a cname record (guessing here) to point to the new server name, but the path must match verbatim. Eaither way, you'll still want to get that old servername out of the sync list and purging the offline DB is the only way I know how to do it.
FYI, you might want to point your offline files at a DFS share, even if you don't have a second target. This way if you need to move to a new FS down the road, it's controlled at the DFS level and won't affect your clients.