CI300 is right, you need to manually update. However, once the tracks are deleted from the Library on the Computer, they are gone for good. If you want to put the tracks back, you will have to re-import them from the original source. I'm not sure whether it's the same on the PC, but on the Mac, before you delete a track, iTunes lets you put in the Trash first, making it at least retrievable until you empty the Trash.
The problem with deleting tracks from the Library is that if the iPod crashes and has to be restored (ie. wiped and reset) by Software Updater, you won't have the tracks on your computer to put back onto your iPod.
AppleMacster