IBooks in Mavericks lost 700 books

For a short while, iBooks Mavericks showed all my books and pdf's. They all disappeared.  I found the directory ~/Library>Containers>com.apple.BKAgentService>Data>Documents>iBooks>Books with about 700 folders, epub files and PDF's.
When I right-click to <Open In> and select iBooks, iBooks tells me the book is already in my library.  But there are no books visible in any of the tabs in iBooks.
Some but not all of the books are on my iPad 4.  I can'f find a way to sync the new iBooks with the iPad.
I hope someone finds an answers. I'm stuck.

I similarly had a very large library that appeared to transfer when I first opened iBooks on Mavericks. Only books purchased through the iTunes store showed up, and attempts to manually add others resulted in the same "already in your library" message, even though they were not visible. Moreover, I can see no way to manage which books to sync with ipad, iphone, etc except through iTunes, and no way to add new books in iTunes, or to edit authors names, cover art, or other metadata. Many of us have large epub libraries, not to mention PDFs, obtained by legitimate means from sources such as Project Gutenberg, Google Books, and other ebook sellers that are not available on the iTunes store.
EBEO's solution is not a fix. The message now is there are no books in iTunes to transfer.
Apple: Please Fix!

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