Q: iBooks PDF's lost after updating to iOS 9.3

How did you update, via a computer's iTunes or directly on the iPad ? If via a computer's iTunes did you copy them over to the iTunes library (File > Devices > Transfer Purchases should have copied them over if though they aren't purchases, and if using a Mac with iBooks on it then done File > Move Books From iTunes in it) prior to starting the update ?

If you don't have a copy of them on your computer so that you can sync them back you will need to redownload them from where you got them from.

No suggestions, I'm in the same position. I do have all my PDF's still on iBooks on the Mac, but see no way of being able to transfer them. I did do a transfer of all books to iBooks from iTunes and there are no more PDF's in iTunes, which I guess must be the reason why they are gone from my iPad.

Sometimes there could be a glitch with iCloud with so many people loading books to iCloud and it may just be the fact that it will need to take time to download them all to the iPad. I have hundreds of PDF's. I have noticed that the last read date on iBooks on my Mac all say March 23rd, which is today. So staying hopeful that it will all right itself over night. Also my iBooks on the iPad just crashes continuously. Every time I open it it closes. I have checked all my settings and preferences in iCloud for iBooks and everything is switched on. Hoping it will work soon, in the meantime if you notice anything else, please do share.

I am chatting with Apple support on Twitter. Will let you know what they suggest. I've also done several hard reboots on iPad and restarted Mac without success.

Apple offered the following solutions to try, but neither worked. Status quo: No PDF's on iPad, PDF's all appear on Mac okay, Books okay on iPad and on Mac, Collections list still showing on iPad as on Mac but no content on iPad.

I also tried to switch of iBook selector on iCloud Drive on iPad for iBooks, then rebooted and still no content.

Plus iBooks crashes when I change collections.

Further suggestions by Apple, ouch!

There are additional steps we can take to get your iBooks up and running properly. The first to reset all the settings on the iPad. There may settings that are crossing up and causing issues. What this effectively does is to reset some of your settings to factory default. It’s not a complete removal of settings. It removes all of your preferences for Wi-Fi, Bluetooth, Do No Disturb, Notifications, General, Sounds, Brightness & Wallpaper and Privacy.

To reset all settings from the home screen open Settings > General. Scroll down to the bottom and tap on ‘Reset’. Select Reset All Settings > Tap button to Reset All Settings > Tap Button Again to continue.

If the reset does not get things up and running as expected, there is likely corrupted data in the iOS. We can replace the operating system with a fresh clean version. You can restore the iPad to factory settings. You can learn how to complete that process here http://apple.co/1L6v9g4

I'm not entirely for certain, but this may be your issue:

Once you update to OS 9.3 and if you also update to OS 10.11.4 when you open iBooks it will ask you if you want to sync your books to iCloud. If you choose "yes," then all of your books that were not purchased from the iBooks store will be uploaded to your iCloud and DELETED from your computer. This can be a very long process if you have lots of iBooks. (I have over 8.5 GB totaling over 2000+ books). Apparently, Apple knows best what data you need on your drives and devices and believes that you have internet access 100% of the time.

Anyway... if you have "Hide iCloud books" ticked on your devices, then it will seem as if all your non-purchased from iBooks store have literally disappeared. They have not. They have just been deleted from your device if you synced with iTunes. If you unhide the iCloud books you will notice that they are all there, but you have to download them ALL again. Yes, you read that right. When you resync to iTunes, those books will no longer sync. But, they also don't show up in iTunes anymore.

To fix this issue, if you prefer to have all your books on your devices and your computer is to either redownload all your your books from the cloud onto your individual device and have syncing occur through that method, OR to turn off iBooks in iCloud settings on your computer System Preferences. BUT, if you do this, I think iCloud will do you the favor of deleting all your books. Thanks Apple!

So... if you have a back up, you have a fairly simple fix:

1.) On your computer, Go to System Preferences on your computer and open iCloud. Click on "Options" next to iCloud Drive and deselect iBooks. (THIS WILL MOST LIKELY DELETE YOUR BOOKS so make sure that you have a back up of them before doing this.)

2.) 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 as a backup in case something goes wrong.

3.) Restore from your backup from prior to updating to OS 10.11.4 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 appear and be resynced through iTunes.

5. After everything is in working order, you can delete the folders you moved to your desktop.

If you get an error message when trying to open a book 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. I found that it stalled my computer (and my internet connection out for some time), as it removed and then restored the iBooks, but they were not in the manual order I had originally put them in my collections. 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 in my collections again.

The folder "com.apple.BKAgentService" contains your iBooks, whereas the folder "com.apple.iBooksX" apparently contains the data necessary for iBooks app to know where the books are and in what order they should be in your collections.

Now... if you are like me and have thousands of iBooks, and you have them manually arranged in collections and want to restore those, you can resync through iTunes. If the books return to the device, but are out of arrangement, you can restore your device from a backup. The problem is that once you updated to OS 9.3, a back up would have been made. If you had opened iBooks and selected iCloud syncing, then this may be problematic in restoring everything. I back up my iPhone to my computer specifically because of these kinds of issues. The back up is in Users/Library/Application Support/MobileSync. If you have a back up from Time Capsule you can restore an older back up prior to the update that will then copy all your iBooks back over in the arrangement that you previously had them.

Sorry for the length of this response!

If you prefer to keep your books in the cloud. check to make sure that you don't have "hide iCloud books" on your device selected. You should see all your books and pdfs reappear, but will most likely have to download them all over again to your device.

I Have same on iphone 6. All pdf gone. Books all fine. I had loads of pdfs in library before upgrade. I have icloud and only back ups to icloud via my phone. Grrr

Greetings,

a simple fix, just change the view selector from list to grid or the opposite and voila!

this is quite easy.

all your our PDFs will appear

you are welcome.

THanks for trying. Unfortunately no joy.

Same problem here. This is very frustrating.

In "Settings -> iCloud -> Storage -> Manage Storage" I can see that all my pdfs are stored in iBooks (641MB), but they do not show in my iBooks app. "Hide iCloud Books" is unchecked.

How difficult it is for Apple to allow us to access our iBooks' documents in iCloud? This is stupid.

THats the polite way. It' pathetic. Are there no Apple employees? I have started to put them to acrobat and upload to drop box as thus is a much more safe system.