Back em up!
Here's what's supposed to happen--in slightly simplistic terms: The music is stored on your computer. When you make changes on the computer the iPod will reflect them the next time you plug it into the computer. If you take all the music off the computer then the next time you plug in the iPod all the music will be taken off of it so that it will match what's on the computer. As odd as it sounds, that's what it's supposed to do.
If you tell iTunes not to automatically update and all that stuff then it won't automatically delete the songs when you plug in the iPod. I wouldn't rely on that to preserve your songs because bad things sometimes happen. You might be tired the next time you plug in the iPod and carelessly click through all the warnings.
There are apps for taking songs off of an iPod, but I'd say since this is important stuff that you want to keep you should back it up to DVD or a hard drive. Always back up things that you want to keep.
If you don't have too many songs you could mount your iPod as a hard drive and back up to that.
