Hi all, and you're welcome. I experimented and was successful in my case, but it sounds like there are various other permutations that may require different solutions. I have a Mac, for instance, and no Windows machine available to try that on. But there are a few key concepts:
1.) It is the bookstoreagent that affects where the books are stored and that disables the Books tab in iTunes. Killing that process is the most important part. If it's not killed, it won't matter what you do otherwise.
2.) Add all the books back to iTunes using File: Add to Library, whether directly from the new iBooks storage directory or from a copy of that directory placed elsewhere. I had thought there might be some other service running that would prevent importing, so that's why I copied the whole directory elsewhere. (For problems with metadata, you should have a number of backups of the iTunes Library files, which is where your metadata is stored. Reverting to one of those should restore it for you. The more you monkey around with the app in a broken state, the more you may lose.)
3.) In iTunes, use File: Library: Organize Library: Consolidate Files to get all your files back into the iTunes storage folders.
4.) I don't think it's actually necessary to delete iBooks. That was simply vengeance on my part. But to delete it, yes, you will need App Cleaner (which is free) or something like it. I frankly don't want or need an iBooks for my laptop, whether it manages the books or not. I find it more sensible to manage my iPhone and iPad content through iTunes. Why should I have to use two applications to do that? Lame-o-rama.
Happy night all! I'm happy to have helped.