wb2, this is probably the best time to do that as everyone is likely to accept this is part of the migration. This is something outside your control and you've tried to keep distribution and changes to minimum. As long as you keep relative path consistent, you shouldn't have too much to worry about. I don't really worry about shortcuts, it is a shortcut, it can be recreated. A bigger worry is data loss. You will need to have a good communication with your customers, explain up coming changes and how it will affect them. If possible, create new file servers, setup DFS, test everything and slowly migrate shares.
I have just completed file server migration and restructured how shares are accessed; I have had complaints about shortcuts, and few other bits, I just took it on the chin and explained this is essential to improve resiliency and performance, and most people where like,oh ok.
vfk