This all started when my pdf's in ibooks were "lost" and not showing up on the ipad. ( I store a few of Nate's medical reports to reference while Googling) I went on a fruitless, FRUITLESS! internet search for the answer to this problem. Lots of people have it, you'd think apple would put out something, but no.
I then went on my computer into itunes to try and see if the pdf's were still there and while searching a window popped up saying "you need to update itunes for new iOs". I did. I then went to update the ipad's iOs and got the ipad equivalent of the "Screen of Death". This is a black screen with a USB cable and a sentence "connect to itunes"
PSA: If you get this screen, you are fucked. I am now restoring my ipad to the factory settings.The Icloud backup was unsucessful and now I am hoping the itunes backup I did on the 15th will work. Lesson learned. Apple is an asshole.

WAY 2 Cool 4 School
Re: apple is an asshole (PSA)
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The good news is that after doing the restore (TWICE) I was able use the data in itunes from last weeks sync to repopulate it.
PDF's however, are still "missing". *sigh* Off to work on this.