I have no real idea, but I'd imagine that any troubles with this software could be fixed by letting iTunes/iPod updaters wipe the iPod and re-format the thing. But I've seen no troubles on my 1st gen 10 gigger.
Music playback under Linux is awful, and this is mostly a really cool hack, not anything enormously useful. yet. It's very cool to add software to your iPod (and I wish Apple would add a calculator to the official iPod bag of tricks), but your inner Jobs will recoil at the interface and slightly clunky controls. Though surely this will only improve with time, and hats off to the folks responsible! It's a very cool development. Has there been anything available for the iPod that so thoroughly hacks the thing? I know there's lots of shareware that adds useful info to your notes or contacts (movie showtimes, etc.) but this is a whole 'nother thing entirely.