Boom! Fixed my problem. I added some books this morning and then everything disappeared except a few in my "docs" section. I couldn't figure out what was going on and since it was a new paperwhite that I'd not used in a couple of weeks and even then only a couple of times, I was thinking it was all kinds of problems.
I deleted all the new books and baam! the rest were back. Then I did the mobi to mobi conversion and everything looks good. thanks! I never would have figured that out.