I had this exact same problem, but for us it was when we moved from 2.0.3 to the 2.1.x series. What I found was that static single pages were fine. The problem was in nested pages.
In the above example, after upgrading to the 2.1.x series, the ONLY page that would show up in the admin was the root Links page. I had to get my admin to "re-assign" all the subpages to the links category. That's the problem, the pages are all still there in the database, but they "lost" their child status to their respective parents.
I have one site to this day on the 2.0.10 series... with about 200 organized pages, that I am afraid to upgrade simply because I neither want to have someone re-assign all those pages, or worse, having to redo them all.
Good luck... but it sounds to me like you will have to have some edit the database and re-assign a parent id to ALL your "missing" pages. It's not a fun job.