iBooks PDF's lost after updating to iOS 9.3

I'm in the same boat. Yesterday after both Mac OS and iOS were updated past the 10.11.4 and 9.3 levels, and I used iBooks, I was asked to use iCloud Drive to store my files, including non-Apple-iBooks-store files like ePubs, PDFs, etc. OK, I see how my iCloud is working for iWorks apps OK. Great, no longer figuring out why I have to now manage the files outside of iTunes and inside of iBooks only to sync them only individual iDevices using still iTunes. iCloud Drive is *finally* useful for me. Then...BAM...all my non-Apple-iBooks-store files disappear. Just like that. After pressing the "Yes, I'll use iCloud Drive" button after launching iBooks on Mac OS or iPhone/iPad.

Like all of you...after decades with Apple, they certainly have lost the "It Just Works" lifestyle we enjoyed under Steve. Now, I get to rebuild my collections by trying to find them somewhere. Or, I can just stop using another app I cannot delete from an Apple hardware. Hmmm, choices.

The best part...providing Feedback to Apple gets you no reply. Typing here we just moan to each other, and sometimes one of us stumbles on a fix that helps a fraction of us. But don't worry, soon iPhone 7 will be here to fix everything 😟

It happens even if you DON"T use iCloud Drive! 😠

Brilliant! that fixed it for me. many thanks

File > Devices > Transfer Purchases fixed a problem that I had syncing PDF files from iPhone to iTunes. Thank you!

I have the same problem. Working PDFs keep disappearing from iBooks.

My solution is simple, I keep a backup copy of each PDF in a PDFs folder in Dropbox.

when the PDF disappears, reload it from Dropbox.

Haven't got time to waste sorting iBooks. iBooks will get fixed sometime!!

Had PDF on all systems but ipad2. I finally went on iPad to settings iCloud, then turn on iCloud, then checked iBooks to on.

Went to ibooks ok and waited. Soon all iCloud storage came up. Selected particular document, and it appeared in pdf on iBooks. Hope works for you.

Acrobat AND to drop box, or as a way to get them to drop box? Will acrobat access and give some sharing feature beyond print and email of the pdfs in iBooks?

ive been loathe to share anything with Adobe but if the answer to above is yes, that might beat emailing all the PDFs in my ibooks to myself and then putting them in dropbox

This is disgraceful on apples fault, they are dong the same thing with user owned music that we long ago uploaded to our iOS devices ...

i am exploring Linux for future des and laptop purchase. Not interested in feeding people who refuse to support me using my data on their hardware.

Note to Apple. Go back and watch the original anti "1984" Apple commercial.

YOU DONT OWN OUR DATA.

After updating to iOS 9.3, not only did this iOS update remove all of the books in my iBooks app, it removed all my music and playlists from the Music app -- Thousands of songs and dozens of playlists.

Apple's suggested "workaround" is to recreate the Playlists. This not a "workaround". This is a bug. Please fix it. It took years to create these music playlists. Similarly, it has taken a lot of time for me to create these libraries in iBooks.

The same comment applies here . The suggestion of re-downloading the books is not an acceptable option.

Apple: Please fix these bugs. As your product quality continues to diminish so does your credibility and future revenue opportunities.

Apple are not here, these are user-to-user forums.

King, you must have left out a word between "Apple" and "are". The latter is used when referring to a plural; if referring to just "Apple" as an entity then the singular "is" should be used. 😉

I'm English, not American

To paraphrase GBS, another case of two peoples separated by a common language! 😁

I Had the same issue. Here's what worked for me. Settings, iCloud, iCloud Drive - for some reason everything was selected "on" except "Books". I turned it "on" and synced both my iPad and iPhone (via USB) to my iMac. All PDF's and other documents returned.

Thank you so much. I switched on my iPad 2 tonight and all my PDFs had disappeared. I haven't changed anything in my settings so didn't think to check this. Very mysterious. Wonder what cause it.

Well, 9.3 update was crucial for many iBooks libraries, especially large. My iPad air2 library of over 3k epubs was ruined. All order was lost, part of books disappeared or lost their covers, the app itself stopped working. I had huge hopes for ios10 after sending them my crash logs, but no. All problems are still here. iBooks is useless for me now, trying other e-readers, Switched to Kindle, then Nook, didn't like them much, now Marvin :-(. Very, very disappointing.