My first thought is that anything on /programs0 or /programs1 won't work immediately after an upgrade - the mountpoints will no longer exist, nor the entries in /etc/fstab that get them mounted.

When I work out how to get the 2.0 software on my player I'll look into a simple restore script. (No linux upgrade software, and the new installshield wont install Emplode on my old Win95 laptop.)