iBooks books lost on iMac after upgrade app

If you choose to sync iBooks with the cloud, then all your books and pdfs will be transferred there from all your devices, including your computer. Any iBooks purchased from the iBooks Store will be the only books that apparently remain on your computer and will show in iTunes. This, of course, results in the copies being actually deleted from your devices upon sync, with the exception of those books purchased from the Apple Store.

To see your books that are now stored in the Cloud, you need to make sure that the option "Hide iCloud Books" is not ticked. Then, you will see your iBooks which you can download to your device all over again. Apparently Apple's engineers can't fathom that if you decided to have that data on your device you might actually WANT it to be there, but instead make the command decision to delete your data and put it all in the cloud... because of course everyone has access to the internet all the time...

To fix this, you can either go through every one of your now uploaded and deleted iBooks and press the cloud icon with the blue arrow to re-download the iBook (I had 8.5 GB consisting of over 2000 books... so imagine how long that would take) - or, if you have been backing up to a Time Capsule or some other device you can restore your books through the following method:

1.) Go to System Preferences on your computer and open iCloud. Click on "Options" next to iCloud Drive and deselect iBooks.

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.

3.) Restore from your backup the above two folders.

4.) Open iBooks. Sign out of your account and sign back in. Your iBooks should be back on your computer and resynced through iTunes.

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), but it deleted and then restored the iBooks, but they were not in the manual order I had originally stored 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 again.

Thank you! This helped me restore my local iBooks collection and get it off of iCloud Drive. I didn't realize what I was clicking at the time, and since I already backup/sync directly with iTunes I had no use for sticking all my books in iCloud Drive.

Anyone else trying to do the above, I also noted that things didn't immediately fix themselves after signing out of the store and back in. I did end up restoring the com.apple.iBooksX folder a second time and then actually rebooted, then launched iBooks and got the welcome screen, clicked on All Books and all my stuff was there again.

I assume it won't bug me again to use iCloud Drive as long as I have the iBooks toggle off in System Settings > iCloud? Do bookmarks still sync at all? Not that big of a deal since I read most everything on the iPad, but it'd be nice to have bookmarks sync with the iPhone for anything I'm juggling there.

A followup on this, I recommend NOT rebooting or anything and just letting iBooks sit open for a while and let it think, even if it doesn't look like it's doing anything. The rebooting thing seemed to help, but in actuality I went and deleted a file in iBooks and then everything suddenly shuffled around and a bunch of stuff disappeared. I *think* rebooting stopped it from finishing rebuilding the library, but not sure. I went through the above process again restoring both folders and the iBooks preferences file, let it sit for a long time, and it seems totally fine now.

Saving a backup of my Book folder just in case...

I have a similar issue. have some 300 books stored in iBooks on my Mac, which I sync on my iPad using iTunes.

The other day I was asked whether I wanted to use iCloud to sync books. I thought what the heck, why not. Now when I checked my iPad today, and wanted to continue reading a book I was reading a few days before ... it was gone. I still have some 30 odd books on the iPad. But when I go to iBooks on the Max, I still see all my books.

I am not clear about how I go about getting those books back on my iPad. I disabled iCloud use for books. But that did not bring them back ...

Your problem seems to be different: your books disappeared from iBooks on the Mac ? In my case, all my books are visible in iBooks on the Mac.

The trouble is that when I connect my iPad, iTunes does not see them ... and so cannot sync them.

Any idea how to recover from that ?

PS: I got badly burned once already with iCloud Music that made me essentially lose my entire music library - thankfully I had kept the originals. I should have known better than try and use it for my books. Apple's idea of a "cloud" service is really goofy.

Sorry, correction to my post. Since I deactivated iCloud drive for books, my books are now also actually GONE from iBooks on the mac.

Meaning they are gone for good! I have a backup, but I don't have it with me (it sits at home).

But I found them all: they are all in /Users/albert//Library/Mobile\ Documents/iCloud~com~apple~iBooks/Documents/ I copied them all back into a new directory (/Users/<user/Books) and opened them all using iBooks. Now they are all back, and iTunes also sees them and syncs them back to my iPad.

Lesson learned: do not trust Apple's iCloud for anything you value. Their logic of what constitutes a "cloud service" is clearly different from anyone else's idea. That applies to books, but also to music and photos. Stay away from it!