Books keep disappearing from my bookshelf

I have this problem too. But different case. It happened when I was importing my pdf files from dropbox (using safari) and then out of no where ibook just auto closed (as usual) and I thought it was just ibook crashed due to overloading or what so ever reason. Thought that nothing to be worried about as it always happen. But when I continue import one of the pdf file in ibook, I noticed all the books that I have imported (hundreds of pdfs) vanished except for that one pdf that I have just imported in after the "crash". Does anyone knows what can I do to recover it ?

ipad, iOS 6.0.1

I too have experienced this several times within the past month. I have virtually ever book I've purchased downloaded to my iPad; my iPhone only has a few titles downloaded due to space constraints. On three occasions, I have opened iBooks and found the shelves empty, forcing me to visit the Purchased Books tab and manually re-download everything.

My books are organized among a half-dozen collections. Interestingly, when I re-download the books, they often return to the collection they were placed in.

Certainly sounds like a syncing issue.

For what it's worth, I tried iMobie's free PhoneClean app (OSX) tonight which deletes cache files and other app artifacts. It freed 800mb on my iPhone and over 3Gb on my iPad. More importantly, iBooks seems to be more responsive now. When I was downloading the remainder of my purchased books prior to my original post, the download icons and animations acted buggy. When I resumed downloading after clearing cache files, things performed normally. If I don't post any further, you can assume this remedied the issue I described earlier.

is there really no solution for this? It is a waste of time to redownload everything manually even it do "sync" back into the same folder.. it still takes time to load and download it from dropbox. especially when you have thousands of PDF files to copy.. 😟

UPDATE: I'm sorry to report that cleaning my devices' caches was not a lasting fix for this problem. Books are continuing to disappear from the shelves and ave to be re-downloaded. I have reported the bug to Apple through their Feedback form.

Ty...I'm seeing the same thing for about a month now. It's gotten progressively worse over the last few days.

I suspect Apple's made a change at their end that wasn't fully tested. Here's hoping they fix it soon!

This is happening to me too. How have they not fixed this?

UPDATE: I reported the issue to Apple using their online Feedback form. Coincidentally, there was a minor update to the iBooks app about the same time. I have not had the problem since. Knock on wood.

This has recently started happening to me.

I had 221 books in iTunes/iBooks. I sync, it seems OK. I open iBooks on the iPad 2 Air (iOS 8.3) and all the book are there for a few seconds. I've even been able to click on one a few times, only to have it close with the error "this resource is unavailable", and then all but 17 books vanish, poof. Sometimes it's 20, sometimes it's 4, but most of the books always disappear.

This is still a problem in IOS 8.4. It is not fixed. I would be horrified if I did not have my full Linux Rsync backup. Apple has been a bit bad in the past about preservation of user data. Nasty.

I wiped my iPad, still no change. This is frustrating. I'm going on vacation in a week and can't even get a reading list on iBooks. Maybe I'll try the Kindle App, I'm desparate.