Music keeps disappearing from ITunes/Mac But Remains on IPod

For several years now, my music periodically disappears from iTunes and my iMac (or previously, my Mac Mini), and it is wiped even from my Time Machine backups. That's weird enough -- and very frustrating. But whenever this happens -- usually with an iTunes major update -- I check my iPod Classic, and the music is still there. Does anyone know why this happens and how to prevent it? A search on my iMac finds the album in question, but it's also missing the songs missing on iTunes. I'm afraid to sync my IPod Classic because iTunes might wipe those songs off the iPod, too.

The music that disappears is not consistent in its origins. The last time this happened, about six months ago, the missing music was a combination of downloaded music from iTunes and Amazon. Although it was a pain, it was easy enough to fix since both sites allow you to re-download music. This time, I'm missing CD music, and that means that I have to identify and haul my CDs out of storage boxes. I'd really like to prevent this happening again. And I really don't understand why the music gets wiped from everything, including Time Machine backups.

My questions: How do I prevent this from happening? If I sync my iPod Classic with iTunes, will iTunes wipe all the music from the iPod even though it is already authorized on this computer? Is there a way to move songs on my iPod to iTunes? (I seem to remember this happening with purchased music, but I don't know if it will work with CD-downloaded music.) And last, a more difficult questions since not even Apple support techies can answer it, WHY does this happen? Might it have something to do with DRM?

I'm running Mountain Lion 10.8.2, but it has happened in both Lion and Snow Leopard. I have the most recent version of iTunes.