I don't use Banshee so I don't know what will happen, but let me get this strait.
You have two partitions setup on your computer, one for windows and one for linux. Windows is the largest partition and is where your music is stored. In linux Banshee is your media player, and you have it setup so that it reads and plays from the music folder or whatever on your windows partition? Is that correct?
If that is the case then it should not try to move your music to the linux partition. All it is going to do is rebuild the database on your ipod, not on your computer; it can already read the database on your computer. What I think it will do on your ipod is erase the current database setup and re-index the files on the ipod so that it knows what is there. In theory it shouldn't do anything to the music files themselves. However, once it does that if you plug your ipod in under windows, iTunes will probably give you an error saying something to the effect of the database on your ipod is corrupted. If you don't want to use iTunes anymore, just ignore it.
Again, I just want to stress this is what I think will happen; I've never been in this situation myself.
Good luck, and let me know how it goes.
Last edited by EricGod48; 04-04-2008 at 04:33 PM.