Copying Content from your iPod to your Computer - The Definitive Guide | iLounge Article will contain all the information you need about extracting from your iPod to iTunes. Personally, I haven't tried it.
And I agree with Ratbastid (of course). I have never heard of iTunes searching for and deleting illegitimate songs, and I'm sure I would have heard the howls of protest all over the Internet if that were the case.
Keep in mind that, by default, iTunes renames the songs when it imports them. Search for words in the song title.
Are you close running out of room on your hard drive? I've seen screwy things like this happen when you are almost out of room.