I can't help with your original problem. To make it more likely that somebody else can, you should mention what operating system and what kind of interface your scanners use (USB, Firewire, etc.). Make sure that the CS2 installation didn't leave your hard disk so full that nothing can work reliably.
As to the new question... software includes application programs and drivers, all the stuff that's stored on the hard disk of your computer. Firmware is what runs inside the device (the scanner in this case) and is stored in some other kind of memory inside the device. The reason for all the dire warnings is that if the firmware isn't valid, the device may not even be able to talk to the computer to correct the problem. There are lots of (mostly bad) reasons why the firmware update process can be very fragile.