iTunes don't show all books

So even after the latest and greatest upgrade, I see the solution is to download all books in Kindle format and use Amazon's reader. I remember a long time ago when iBook's was useful. It's not worth the effort.

Download or convert your books to kindle formats. Select your device in iTunes, go to apps. Scroll to the very bottom. Select the kindle app. Hit the add button an add the books you want. Hit apply or sync. Take your iPad and go, secure that the books are there. Move iBooks to a sub folder, so you are no longer tempted to touch it.

Download Calibre or other library program and store your books there.

Hope this helps. I feel your frustration.

I have the same thing. On my Mac's iBooks app, I have hundreds of books which I have mostly loaded, but some are purchased from Apple. They show up on my iPad and iPhone. On my iTunes, I see 4 books. I have "all books" selected, and I'm showing "Books and PDF files" (but those 4 books are not pdf files). I don't see any way to tell iTunes to select other books only.

Thank you so much for this tip. I hadn't gotten around to thinking of doing a Spotlight search for epubs, and believed my books were gone forever. They showed up as you described, and I saved them to a folder that Apple hopefully won't find and destroy.

It's some other iPhone-compatible book reader for me. I'm sometimes away from decent access to the cloud, and I don't want to depend on the good graces of Apple to look after my best interests and preferred ways of doing things. I remember when iTunes and even iBooks were relatively simple, straightforward applications that did the relatively simple, straightforward things I wanted them to do.

This is because you chose the option to sync your iBooks with iCloud. This deletes everything with the exception of iBooks purchased from the apple store. Apparently Apple knows best what should or should not be on your computer and your devices.

You will also find that on your devices, any iBooks that are not purchased through the iBooks store will need to be downloaded all over again (click on unhide iCloud books--they will have the cloud with the downward blue arrow). I had over 8.5 GB of iBooks this occurred with. Irritated is hardly the word I would use about this.

You have two options:

1.) keep your iBooks in the cloud and when you want to read one of your books on your device, download it from the cloud all over again. If the book was not purchased from the iBooks store, it will no longer show up in iTunes on resync. (At least that is what I found to be the case on my computer). This is especially annoying because I don't always have internet access... and that Apple made the command decision to delete all 8.5 GB of data from my devices really concerns me. They should have at least provided the option for ME to choose what to do... or clearly indicated that this would happen if I chose to sync to the cloud. They did neither. I'm highly irritated about this and wonder what their engineers are thinking!

2.) Do the following on your computer if you have a back-up on something like Time Capsule or another drive:

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

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 to back them up in case something goes wrong.

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.

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. The folder "com.apple.BKAgentService" contains your iBooks while the folder "com.apple.iBooksX" apparently contains the information necessary for iBooks to know what books and in what order in the collections they appear. They will also reappear in iTunes.

I had to then complete an additional step as I had synced my devices through iTunes which resulted in all 8.5 GB of my iBooks being deleted as Apple thought I should download them all individually again from my iCloud. I had to restore my devices from a back up. This could prove tricky if you have iTunes set to automatically sync when your device is plugged in. If that is the case, you should check the option in iTunes preferences to stop automatic syncing when the device is plugged in. Also from a back up, find your MobileSync folder in your User/Library folder and copy those over to its equivalent on your hard drive (making sure that you back up the original one that was there in case something goes awry). Then, restore your device from the copied over back-up. The reason to do this is because if you updated to OS 9.3, then it would have replaced your original backup of your device with the one where you chose to sync to the cloud. Once you have restored your device, your books should copy over again and everything be back to normal.

Hope this helps. Sorry it is so long :-)

So I wonder what I did right then...

After updating to IOS 9.3 on my iPhone 6 and my IPad Mini 4, and to OSX 10.11.4 on my late 2012 MacBook Pro, I selected to use iCloud for iBooks on all three.

All my non-iTunes epubs are still on my iPhone 6 and my iPhone Mini 4. On my Mac, I can see each non-Apple book just fine iBooks. No cloud symbol in the corner. Each opens immediately without having to be re-downloaded. When I go to the "com.apple.BKAgentService" folder in the finder, I can see that my non-Apple epubs are no longer in that folder, but when I search for "epub" in the Macbook's Finder, all my Apple and non-Apple epubs show up in the results list (and now the non-Apple book files actually have the real titles back instead of the strange number codes that the Apple epubs have). The pathway for each of the non-Apple epubs shows as: iCloud Drive > iBooks > [Book title].

So I thought, well, maybe they are on the iCloud drive and I will not be able to access them if I don't have internet. So I shut off my internet connection, then went to iBooks, and opened a bunch of my non-Apple ebooks. All of them opened just fine, no problems, no errors. I did not have to re-download a single book. So as far as I can tell, there MUST be a copy of each epub stored locally somewhere on my computer.

Lastly, when I connected my iPad Mini 4 and iPhone 6 with my MacBook Pro today to sync them, all my books (including all my non-Apple epubs) showed up in iTunes and all synced just fine. I did notice that it re-synced all 52 of my non-Apple books to each device. (And that was because something in the switch over to iCloud it reset the "Category" of each non-Apple ebook from "Fiction" or whatever it was to "Books"). But still, even after that, every book I have, Apple and non-Apple alike, were available on each device without having to re-download any of them from iCloud.

As far as I can tell, it's working perfectly. So again, what did I do right?

You are very lucky then, indeed!

When I did this on my iPhone, iPad and computer; it took quite a while to upload all my eBooks to iCloud. They then disappeared from iTunes, and were not on my computer, but in iCloud. They did show up on my computer just fine. But, syncing my devices to iTunes deleted the books from the device and every book on the device showed up with a cloud icon and the download arrow. As I have over 2000+ books and pdf's the LAST thing I had the patience for was to redownload all those books and was quite irritated that Apple's engineers devised such as system that arbitrarily deleted my personal data from the devices. If I had not noticed the issue, it would have been a big head ache as I am frequently in areas without internet access and would not have been able to have accessed those books/pdf's as there would have been no way to retrieve them from the cloud.

I believe that your iCloud drive is stored locally on the Mac. So the books are probably moved there. But, they were not showing up in iTunes for me and on my devices, all 2000+ books and pdf's would have required me to redownload them. I tested it, and downloaded several books from my iCloud again, and noticed they did not show up in iTunes, but the iBooks purchased from the iBooks store did. While the books that I had redownloaded from the iCloud remained on the device, they were not in iTunes.

I followed these instructions, turning off iCloud Drive iBooks syncing, restoring the two container folders from prior to the installation of 10.11.4, and signing out and then back again to the iBooks Store in iBooks (and, for good measure, signing out and in to the iTunes store as well in iTunes). Nonetheless, iTunes still refuses to show the complete contents of my iBooks Library on my Mac. It only shows 132 of the 631 books in my iBooks Library.

The only way to get books from my iBooks library on my Mac to my devices now is to side load them via an email attachment or by putting them on Dropbox. The side-loaded books then show up for the device under On My Device > Books in iTunes, but still not under Settings > Books.

Michael, if you have the iCloud app enabled, (from settings, iCloud, view app on home screen), you can drag the Epub file into your iCloud folder on your computer. then open the app on your device, and hit "copy to iBooks." it's an easier side load rather than navigating dropbox.

True enough, but that scenario means my book is now using up twice the space in my iCloud account than it otherwise would, since it is also in the hidden iClouds book library associated with my Mac. And it doesn't solve the essential problem: that iTunes misrepresents the contents of my iBooks library.

I should've clarified that you delete the version in your iCloud folder afterwards and it remains on your device. Then, (if you have it set to manually manage), when you sync it BACK to your computer, everything should appear again.

That's how I do it because otherwise it'd be a headache.

P.S. I reverted back to 10.11.3 because my highlights weren't syncing either (and some books were disappearing), but I had a time machine backup. .4 is trash because third part downloads don’t sync properly, and the whole point is to sync third party downloads.

Reverting to 10.11.3 is not an option for me, I'm afraid: I write about Apple stuff for a living, so I rather have to have the latest OS installed. BTW: here's the piece I wrote about the current iBooks, which describes a number of the issues I encountered: http://tidbits.com/article/16378

My work around for syncing imported epub documents (books not bought at iBooks store)

First be sure your books are still on Mac. Open Finder and search for epub files. Imported books should appear with a path iClouddrive>iBooks>Booktitle.epub (Different then purchased books. This, I think, IS THE GLITCH)

1. In iTunes select device to be synced. Uncheck sync automatically when this iPhone is connected to iTunes.
2. On Mac open System preferences and select iCloud>iCloud drive>Options. Uncheck iBooks
3. Recheck iBooks and then all books should appear in iBooks on your mac and in iTunes. (They do for me)
4. Sync ALL books to your device. (in my case my iPhone 6s)
5. I have to go thorough this procedure EVERY-TIME I sync my phone, hence the unchecked automatically sync in 1.

Not a solution but a workaround.

So I had not been using iCloud Drive before, but accidentally turned it on when PDFs syncing became available. I have noticed that the re-downloading did not occur for every book, only the books I had last edited/read, which makes sense because they were updated to the Drive. However, I do most of my reading during my commute and do not have access to the internet at all times. Even after I re-download them, and then turn iCloud off, they disappear again; where I am downloading them to then, I don't understand.