I haven't had this problem myself, but you might want to try changing the option of having your iPod automatically update when connected to the computer.
You can do this by hooking up the iPod to the computer it is currently working with, loading itunes, and in the lower right hand corner of itunes there should be an ipod shaped icon. When you click on this, there should be an option to turn off automatic updating.
I think you were getting that error message to prevent you from plugging into another library and accidently deleting a bunch of songs.