You lost me in the first sentance!! As for Linux, I wouldn't know where to begin. If you think that this might be the way to go, more information would be gtatefully received.
The switching between OSs hasn't caused any problems in the past 3 years that I've had the device.
From what I could glean after an afternoon trawling the web, was that there was little knowledge out there. Rockbox seem to have a fix for it but it just doesn't work on my drive for some reason. No matter what I try, nothing works. Formatting the drive doesn't work either.