Just went through this lovely process two months ago. We used a product called B*Nator, it worked good for us as most of our users are in remote locations. It sent out a wipe command, removed the user from the Domino BES to the new Exchange BES, applied the desired IT policy, and then reactivated the user to the new BES, all automatically. Backups can not be converted from one SQL database to another, I confirmed this with RIM. So users will lose all customization. Are you currently syncing your NAB with your devices wirelessly?