Regarding the software - I would copy the disks to make sure they copy with no errors. Post what the labels say and someone should be able to tell if you have what you need. Hopefully one disk is a backup disk - you might need that to get the commutation numbers listed in the MOC.cfg file if someone changed motor or resolver and didn't update the label under the side cover.
Batteries - During bootup, the controller checks the voltage of the batteries. This is a warning and does not effect booting. It is an indicator that battery voltage may have gotten low enough to effect the memory.