iBooks PDF's lost after updating to iOS 9.3

I have the answer if you selected to upload everything to iCloud:

Mac

Available ePub, iBooks Author books, and PDF files in iCloud Drive automatically download to your iBooks library.

If you turn off iBooks in System Preferences > iCloud > iCloud Drive Options, iBooks items that you save to iCloud Drive will no longer be available on that device.

This was turned off for me. I wasted 2 hours and this was all that needed to be done. It is not set to enabled as a default.😠

After 3 hours on the phone with the Apple support, they realized that they couldn't help me (I knew it from the beginning), so their engineers took over my case. Since last Thursday they have access to my Apple ID and are trying to figure out how to get my pdfs back.

I am having this problem as well and just got off with Apple Support.

I was able to restore the ibooks PDFs from a Time Machine backup by restoring the books in this folder:

Click GO

Option Click to get to Library

Containers

com.apple.BKAgentService

Data

Documents

Data

iBooks

Books

"Books" is where iBooks stores your PDFs. Open "Books" folder then open Time Machine, go back in time before the latest update, and restore all of the PDFs.

Now, I open iBooks and the app is NOT finding and displaying those books. The agent is getting back to me on how to fix that problem, I will update this post when I hear back. Fingers crossed that it will actually work with all meta data in place!

I had the same issue. I upgraded my iPad 2 (old!) to iOS 9.3. At some point a few days ago, it asked me if I wanted to sync iBooks through iCloud, or some such. Thinking this was a good thing, I said yes, and discovered yesterday that all of my PDFs had vanished off of my iPad. Luckily, they were still on my Mac when I opened the iBooks app on there.

But, I couldn't figure out how to export PDFs out of iBooks on my Mac en masse, so here's what I did to get them back onto my iPad:

- Using the search box in Finder, I looked for all PDF files on my Mac. I discovered the files were in a folder called iBooks on my iCloud drive.

- I looked in my iCloud drive folder, but there was no folder visible called iBooks.

- I went to this site to figure out how to show hidden files, but when I looked the iBooks folder still wasn't visible in my iCloud drive

- So, again searched for PDFs across my whole Mac using the search bar in finder. Control-Clicking on one of my PDFs, I chose to "Open containing folder"

- In the containing folder (iBooks - but hidden and inaccessible), I copied all of the files in there. (And promptly backed them up to Dropbox.)

- Then, I pasted all of those files into a brand new folder I created and named iBooks on my iCloud drive, thinking that perhaps it would replace the hidden an inaccessible folder somehow.

This worked! When I went to my iPad, it again asked me if I wanted to use iBooks for iCloud. Figuring I had nothing to lose at this point, I said yes again, and all of my PDFs reappeared in iBooks on my mac after it seemed to do some kind of syncing over the air. When they reappeared, they were all sorted the way I had them originally, so I seemed to be no worse off than before. (I then went back into Terminal and did the commands to hide the hidden folders again.)

My only guess is that the iBooks / iCloud syncing doesn't work well with older hardware - the iPad 2 in my case - even though it's still being supported through iOS upgrades.

Moral of the story after 2 hours of work? I've learned the hard way to not have critical files synced only through Apple-based syncing systems, since so much buggy stuff happens behind-the-scenes, ostensibly to make things easier.

that you have an iphone 6 won't be the problem. i have similar issues and even bought a iphone 6s (as a last resort) thinking that maybe my phone is "broken/at fault". it doesn't freaking matter. the ibooks issues are still there.

Unfortunately I don't have a Mac, so no Time Machine for me.

Apple Support's engineers are trying to fix my for the last 30 days, but no luck so far. They even have access to my iCloud account.

What's amazing is that I can see in my iPad that all my pdfs are stored in my iCloud drive (Settings -> Storage -> Manage Storage -> iBooks (under Documents & Data)). It's unbelievable that not even the people at Apple support can't simply access that folder in my iCloud. Gosh, what a useless cloud storage iCloud is. Dropbox is light years ahead.

How do you access them? My appear on icloud, but can't download them to either my phone or mac. Is there another way to access it and get them to a safer place? I'm so upset I can't get my books.

i am too suffering with the same problem. i had 100s of pdfs and ebooks in my iPad mini,it was ok but on one fine morning when i had opened iBooks i was shocked to find that i have lost all of my iBooks contents...though i have backed them up on iCloud but still unable to restore them.....apple *****....iBooks is the worst app.... it is so frustating....really disappointed with apple,,,,,plse help---

Try changing the iBooks view selector from list to grid or vica versa. It worked for me .

See books and PDFs you add to iBooks:

• On your Mac: Choose Apple menu > System Preferences, then click iCloud. Click Options next to iCloud Drive (make sure iCloud Drive is selected), then select iBooks. In iBooks, click Use iCloud in the dialog that appears.
• On your iOS devices: Go to Settings > iCloud > iCloud Drive, then turn on iBooks. iCloud for iBooks requires an iOS device with iOS 9.3 or later.

Ok, so I found a way that works, but requires that you have backups of all of your ePubs and PDFs. Just remove them from iBooks (delete) and add them back again. Problem solved. Hope this helps.

Hey thanks, this was the only helpful solution in this thread. I copied all the books in my iBooks folder to another folder, then deleted all the books from iBooks app and chose the "everywhere" option. Copied all the books from my backup folder to the iBooks app and suddenly they all appeared in iTunes again.

So thanks!

Hi, when you say the everywhere option, what do you mean? I've been unable to transfer them from iBooks on my mac back to iBooks on the iPad too, so i tried the iCloud drive + delete that you did.. Just not seeing anywhere to click everything!

Hi,

Would it be possible for you to post steps by steps instruction on how to do this, it would really help everyone ?

Many Many Thanks.....

When you delete items from iBooks it will ask you to confirm and show two buttons, one is "cancel" and the other is "Delete everywhere" meaning the item will be removed from all of your synced devices.