Q: iBooks has suddenly stopped syncing between my iPhone and iPad

My thoughts exactly. More and more often, it seems, things don't "just work" anymore.

I'm having a very similar issue. 

iMac OS 10.11.4 with iBooks 1.5, I drag'n'drop an ePub file, and it works.

iPhone 6s IOS 9.3.1 (13E238): iBooks 4.7 syncs.

iPad 2 IOS 9.3.1 (13E238): iBooks 4.7 DOES NOT SYNC.

iPad mini IOS 9.3.1 (13E238): iBooks 4.7 DOES NOT SYNC.

iCloud is active on all devices.

Purchased books sync, only other files (pub, pdf, ...) are missing.

I earlier posted that mine was syncing again.  Well, it does sometimes and not others.  It seems to work after closing a book with the most current bookmark, then force closing the app on all devices.  Then when opening it fresh, the current bookmark will be displayed... but not every time.

There is something going on that Apple needs to address, I think..

It's frustrating.

After installing iOS 9.3.1 and Mac OS 10.11.4 the iBooks sync is NOT working at all:
- MBP 13" Mac OS 10.11.4, iBooks 1.5 (1110.10.4)
- iPhone 6S iOS 9.3.1, iBooks 4.7
- iPad Mini 2 iOS 9.3.1, iBooks 4.7

«No comments», Apple .

Yesterday after many frustrating hours I finally got mine to synch by force closing iBooks on both my iPad mini 4 and iPhone 6Plus. I haven't tried anything new yet but I hope it continues to synch. One book is not loading on my iPad after removing it and trying to add.

I spent time on the phone with Apple customer support yesterday after initiating a service request through the Apple Twitter support account. Apple does not have a resolution to this issue yet and is trying to figure out what is going on.

For me, the syncing problems also started after I downloaded iOS 9.3.1 last week. I, too, tried all of the usual steps (signing in an out of iTunes on my iPhone 6s Plus and my iPad mini 4, force closing the iBooks apps on both devices, toggling syncing, etc.), Then, I took the nuclear option: I completely reset both devices and set both devices up a new devices. (I had iCloud backups for both.) At that point, iBooks not only still failed to sync, but it also wiped out all highlighting/notes, bookmarking, last page read: everything. All 209 books in my collections, all of which I purchased through iTunes, now appeared as brand new books with the little blue "New" triangle in the upper right corner of each book's icon.

One issue to consider: I have different Apple ID's for my iTunes account and for my iCloud account (which is common for people who had iTunes accounts prior to iCloud/MobileMe). I wonder how many others on this thread have the same set up and, if so, if that might be at the root of the syncing failure issue we are all experiencing for iBooks.

That's an interesting theory, and it's one I've wondered about in the past day or two, also. Like you, I have two Apple IDs (for the same reason). I've tried signing out/in on both accounts on all devices, but so far that isn't the solution for me, at least. I'll be interested to see if there is a fix or whether Apple will have to issue an iOS update.

I don't think that the problem is related to multiple accounts (iCloud/iTunes).

Bookmarks, Pages, Notes (in iBooks) are supposed to sync with iTunes Account. Like it worked before.

As I said, Apple will try to find why there is an issue. Like they did before with iMessage, Safari or any other bugs we may have seen in the past. If the problem occurs on every device with iOS 9.3 or 3.1 it's clearly an issue from Apple. So we don't have to worry about, we just have to wait

I wonder how many others on this thread have the same set up and, if so, if that might be at the root of the syncing failure issue we are all experiencing for iBooks.

For reference, I use the same Apple ID for both iCloud and iTunes. I have the same sync issues as everyone else in this thread. Ugh.

Good to know. I do wish, though, that it were possible to merge Apple IDs when the same person has two. Maybe someday.

I can say for sure that the problem is not related to multiple accounts. I have only one Apple ID for everything but my notes, highlights, reeding position and so on are not synced between my MacBook Pro Retina and iPhone 6 Plus (both having the latest OS). I have tried everything: turning off and back on the settings, deleting the books, force closing the app and even restoring devices and so on… Nothing helps!

I should note that if I add a new book, the book appear on another device via iCloud. But notes, highlights, collections and reading position are not synced between the two devices. They are just separated one from another. I mean, for example if I highlight a phrase in iBooks on Mac, it remains highlighted there, but not in the same book on iPhone.

I think the problem is in iCloud itself.

Im also having this issue, bookmarks, read position and notes are not syncing between ipad, iPhone or Mac. none of the usual fixes have worked for me either. It must be something apples side. Very frustrating though.

Just add my voice to this thread, I to have this issue. I've tried everything that's been mentioned, including a clean, as new install of an iPad. Nothing makes any difference. I had a support called with Apple yesterday and they are escalating the issue and I should hear back more in a few days. I'll update as soon as I hear anything. I suspect we'll have to wait for iOS 9.3.2 though.

I suspect you're right, samfromsheffield. I'm as frustrated as most others here, but I try to remember that this is probably not a problem that would worry people in third-world countries. At least we do have our devices and our ebooks, and I trust Apple will come up with a fix as soon as possible. Fingers crossed!

I wonder why Apple is silent regarding this? As for the «Safari link»-bug appeared in 9.3 (when the links became irresponsive), they at least promised to resolve that issue, which they did in 9.3.1. But now they seem not to know about that issue. I have posted several feedbacks here: http://www.apple.com/feedback/ibooks.html , and I advise and ask you to do the same .