Offline files sync issue with server upgrade

Ok,  I have about 20 workstations in the office.  All are either Vista or Win7 and we have w2008r2 for our file server.  Basically when each pc was originally hooked up to the domain the sync automatically sync'd up to our old file server which was server 2003.  Everything was working great until we upgraded the file server.  I copied everything from their current home directory to the new home directory and set group policy to map users to the new server.  What happened is that the sync to the old file server was still in place as offline files on the local machine.  So when users went to find something or save something the default my doc, music, etc.. was pointing to the old file server (this was taken offline) by pointing to their local drive.  So what happens when I go to issue them a new machine, all their files on the server are missing because they have been saving all of their files to their local machine (aka home directory).  This also means that their files are not being backed up as well.  My question is how do I move all of their files from the old machine to the home directory and sync them properly.  I disabled the sync on my workstation and every time I tried to find a file or open office or adobe it took about 3 or 4 minutes just to open a file or folder.  I then copied my stuff over to the new home directory and ended up with many copies of files etc...  then I had to turn the sync back on just to get my computer to run anything with any amount of speed.  This was a really messy process.  Still not quite working well.  Does anyone know how to fix the workstation to point to the correct directory and copy the new files to the new home directory without Pulling my hair out trying to get everything sync'd correctly to the new server without losing files.