No it wont do that.. Once you fire up itunes, it will search for your ipod, then load the files from your ipod into its folders, even if it did wipe your tunes, You still have the folder in itunes..
Ive been using ipods since day dot & never had this problem yet..
The other way is, DONT install itunes, connect your ipod to pc & it will see your ipod as an extra drive..