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Helpful answers
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Mar 30, 2016 3:56 PM in response to Jet787by AndreR.,I had the same problem. After 2 hours on my phone talking to the apple support, they ran out of options and told me to erase my iPad and restore it from my latest iCloud backup, which I did. At first everything looked good on my iBooks, but then some pdfs started to, once again, disappear. Unfuckingbelievable.
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Apr 1, 2016 3:26 AM in response to Jet787by patricgj,I had the same issue - I opened ibooks on my ipad air 2 some days after upgrading to 9.3.1, and it asked if I wanted to sync using iCloud (don't know if it said icloud or icloud drive). I said yes, and immediately a large part of my pdf's disappeared.These were only present on my ipad. Also some books were gone.
Somehow I thought of going to settings - icloud - icloud drive and turned the toggle OFF for ibooks.
Now all missing pdf's and books are back again.
I'm afraid to sync with icloud drive again - I think they'll disappear again. So, basically, I can't use icloud drive with iBooks, because half of my content will be gone.
Edit: Tried it, turned the toggle back on: and now it's syncing properly.
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May 9, 2016 10:07 AM in response to patricgjby Rishi Khanna,I had the same issue but after unchecking the iBooks under iCloud Drive, my pdf's still have not recovered. Interesting thing is that it appears the files have not deleted from the iPad cos the amount of available space has not increased. My pdf data may still be there.
I am trying to see if i can recover the data without restoring it from the cloud.
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May 11, 2016 10:40 AM in response to Jet787by mayree49,I have the same problem except my PDFs don't show up on my PC iCloud drive either. Although my Pro settings indicate that they are in iCloud....so frustrated.
iPad Pro 9.7, 9.3.1.