Will updating my iPod delete my files?
No. Upgrading iOS should leave the files that are on the device in the exact same condition as it was before. That said, however, it is always important to do a backup of all the data on the device before upgrading. 

When you plug your device in, open iTunes, and select the backup option, it should backup all the data that is on your device, including any music that is not in your current library. Note that this will not add that music to your library, though, it just saves it in case you happen to need to restore your device at a later date.