ios 9.3 deleted my files from ibooks on ipad.

I lost over 550 books on my IPads following the IOS 9.3 upgrade and sync. I have 675 books in my Macbook Pro Library, but now only 202 books on my IPads, and when I sync, they do not come back from my Library despite have "Sync All Books" checked, and "Hide iCloud Books" unchecked. And the majority of books on my IPads show up with the iClous icon in the corner. Any ideas on how to get them back from my Library?

If you have a back up to Time Capsule or some other drive try:

1.) Go to System Preferences on your computer. Select iCloud and then next to iCloud Drive select options. Scroll down until you see iBooks and deselect it. This will prevent iBooks on your computer from syncing with iCloud. BUT first make sure that you have a back up of your books because I think this will delete your iCloud books.

2.) On your computer, go to Users/Library/Containers and find the folder "com.apple.BKAgentService" and the folder "com.apple.iBooksX." Copy these two folders to your desktop just in case something goes wrong. It might help to restart your computer at this point.

3.) Restore from your backup the above two folders "com.apple.BKAgentService" and the folder "com.apple.iBooksX."

4.) Open iBooks. Sign out of your account and sign back in. Your iBooks should be back on your computer and resynced through iTunes. You might have to close iTunes and reopen it and go to your devices and then "Summary" then "Books" to make sure they are all appearing there.

If you get an error message when trying to open a book in iBooks that it can't be found, or all your books begin to disappear again when reopening iBooks on your computer, wait and let the app finish what it is doing. Be patient. I found that it stalled my computer (and my internet connection out for some time), all my books disappeared before my eyes (which was alarming!), but then iBooks restored them as I clicked through my collections. They were not in the manual order I had originally stored them in my collections though. To fix this, I closed the program and copied the folder com.appl.iBooksX over again. When I reopened the app, everything was in place again. Apparently, the folder "com.apple.BKAgentService" contains your books, whereas the folder "com.apple.iBooksX" tells iBooks on your computer where you have them and in what order they are in your collections. Once you have ensured that everything is in working order, you can delete the folders you put on the desktop. Doing this should then restore everything as it was to your device.

A final note: I had synced my updated iPad and experienced what you did--all my books had been deleted and moved to the cloud, and each book had a cloud icon with a downward pointing blue arrow. As I have over 2000+ books, it would take some effort to redownload each one individually. And, my resyncing them as described above put them all out of order in my collections. To fix this, I copied an older back up of my iPad into the User/MobileSync folder (I moved the newer one to my desktop just in case something went wrong) and I restored the device from the older back up. All my books then copied back over as they were before to the device. You should not have to do this step though unless like me, you have thousands of books that you don't want to take the time and effort to reorganize manually. I should mention here that I backup to my computer rather than iCloud specifically so that if anything goes wrong I have the backups on hand.

Gene, Thanks for the reply. Unfortunately, my problem must look/be a bit different. In my Macbook Pro iBooks Library, none of the books have the iCloud icon. That is only on the books on my IPads. And per your step 2, I have no path/directory to Users/Library/Containers, even when I tried Finder Go To Folder (I also checked under each of the defined users on the system). So I was unable to locate the folders you mention, and copy them to my desktop. I should mention I am running OSX 10.11.4, perhaps that makes a difference. So I did not change the setting in system preferences, as I could not find the folders to back them up. I may be doomed to downloading the books one-by-one to my devices. However, my concern is if I ever run an iTunes sync again, will the books all disappear again and doom me to a lengthy download session?

The Containers folder should be in your User/Library folder. Not your main Library folder. For example, on my computer it is located under /Users/genesurber/Library/Containers

Also, the "com.apple.BKAgentService" and "com.apple.iBooksX" would need to be from a back up previous to your upgrade to 10.11.4 and opening of iBooks to tell it to sync with iCloud, not afterward. The folders that you currently have in your containers folder don't have your non-iBooks store books in them as they have been moved to iCloud.

The books in iBooks on your computer will appear as they usually have; however, if you have iCloud sync on they are actually stored on your iCloud drive.

The books on your device have been deleted as well, but you can re-download them. I did a test on my iPad and downloaded a book from iCloud and it remained on my device after syncing with iTunes. But, the book did not show up in iTunes. The only books that appeared in iTunes were the ones purchased from the iBooks store.

I, too, am running OS 10.11.4.

I was in the same situation, I had stored 100s of books iBooks, some pusrchueoed from iBooks some not. Lost about half of my library. Very much unacceptable Apple! Thank you very much. After hours of digging I got lucky and was able to recover my library. This is what worked for me. On your Mac, type following two commands into terminal :

cd ~/Library/Mobile\ Documents/iCloud~com~apple~iBooks

open .

This should open a folder for you. If you are lucky there is still chance that your books are stored there. Good luck.

I was wondering where Apple had moved all the books. I figured it was in the iCloud drive, but the iBooks folder is 'hidden" by default. Grrr.... Least the books in there now use their real names instead of some string of numbers you can't decipher.

Now if Apple would just get it's act together and allow metadata to be edited in books like you can Moves, Music, etc.

Question is -- there are still ebooks in the com.apple.BKAgentService container -- looks like those are all store bought books though. Is the com.apple.BKAgentService directory still of use?

Whereas ALL non-store books were moved to the hidden iBooks folder.

And now to break out my terminal-fu and make the folder visible...

Hrrmmm... Since we really didn't seem to have a choice with this move, I wonder how the space used by iCloud for iBooks counts? Is it "free"? or count toward your limits?

So, nohidden terminal command does not seem to work with this folder. However, once you have opened it as stringcode shows above, you can drag the iBooks folder icon to your sidebar in any finder window. That will give you quick access to your iBooks stored in iCloud whenever you want.

Thanks, this was very helpful. I managed to find the directory iCloud~com~apple~iBooks using terminal. It has a sub-directory called documents which holds the actual pub files. I managed to open this last directory in Finder using the open command, as you described. I have copied all the pub files to another directory so using that I should be able to get iBooks sorted again.

Try deselecting "hide iCloud books." You should find all your iBooks and PDF's there again... but you may have to redownload them to your device.

Do you have any bookmark/note syncing problem after you retreated from storing books in iCloud? I can't sync anything.

Did that, still no sign of them, seems they are lost forever..