As far as I know, there is no way to prevent that. I suffered hours of headache reloading a full 30 or 40 gigs to a friend's iPod (on USB 1.0, no less!) after iTunes randomly decided to wipe the whole thing while I was trying to configure it to work with a laptop instead of a desktop.
In addition, if you try to load one song too many on, and it warns you that "There isn't enough space... would you like us to choose all the songs you don't want and copy them three dozen times each, etc..?" button... one wrong click erases the whole iPod and sends your synchronization back to the stone age... Very frustrating interface for PC users. I rarely use mine any more.