IBooks deleted books after sync

Okay, this one's bizarre.
I have a fairly large ebook collection, about 300, consisting of purchases from the iBookstore as well as other free epubs, non-DRM epubs purchases from places like Fictionwise plus various pdfs. Yesterday after syncing my iPad (which included about 30 app updates and 2 new books from the iBookstore) I opened iBooks to witness the following: while the little "working" icon was spinning in the menu bar, about 80% of my books just winked out one at a time and disappeared, one after the other, until most of my shelves were empty.
iTunes was set to sync all books, as always.
When I went back into iTunes to re-sync them, they did load back onto my iPad but all jumbled up out of order.
Further examination revealed that all my videos had disappeared too, even though nothing had been changed on the iTunes settings.
Latest version of iOS, latest version of OS X, latest version of iTunes.
Has anyone else had this happen, and can anyone offer any clues? This was a royal pain in the butt, and if possible I want to take whatever steps to ensure it won't happen again.
Cheers,
Chuck

If you haven't gone back in and reordered or reloaded what you thought were lost books, try rebooting your iPad. It cures many "odd" ills. Hold the power and home button at the same time for at least 10 seconds (hold past the swipe to shut down bar if it appears) until the Apple logo appears, then let go of both buttons and your iPad will restart. Check and see if your Library is back and in order. This has happened to a few people and rebooting seemed to solve it for them.......

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