My PDFs disappeared from iBooks after upgrading to iOS 8 on iPad Air

I've just upgraded my iPad air to iOS 8, via iTunes, and restore process. I had a fresh backup, so my iPad has all on it just as before except my PDFs in iBooks. There are just the purcheses in it. Is there any way to get my files back?

All; I had the same exact issue and there is a quick remedy for this which I'll outline below. Even the Senior level tech at Apple was unaware of this and I figured it out myself.
Once your iPhone is connected to iTunes and docked to your Mac, you'll note that there exists a tab, 2nd from right in iTunes 11.4 named 'Books.'
Select this tab and you'll note all of your purchased books and PDF's you've previously chosen to reside in iBooks app on iOS devices are displayed as a mirror image of what actually resides in your iBooks App that by default should result in your doc on the Mac. You must SELECT all or check individually each respective book or PDF document that you wish to sync with and reside on your iOS device.
Just as is the case with Music or Photos you may elect to manage your library of books and apps MANUALLY. In my case there are certain apps I know I want on my iPhone; conversely, there are apps I want to reside ONLY on my iPad and NOT on my iPhone 6. So this is how you control and manage this aspect of the "iBooks" app or program . It's easy!
Good luck!

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Message was edited by: Redwalljp

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As far as I can work out, from incomplete downloads, ticks denote all downloaded ok.
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http://help.apple.com/ipad/5/interface/ the ipad manual (not the used guide - this is more about how it operates)
may prove usefiul to you.
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My PDFs disappeared from iBooks after upgrading to iOS 8 on iPad Air

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