If you sync it to your iTunes library it will remove everything on it.
There is software that lets you transfer everything on it to your computer, then you can add it all to your iTunes library and then sync it all back to the ipod with the media currently in your iTunes library.
if on a mac expod seems to work well and it's free. Used a few times when my external hard drive with all my music on it got corrupted and I had to reformat the drive. Thank God every thing was on my ipod.