Why are books in the cloud disappearing from collections

i THINK that I have figured it out a way around the iBooks bug--because it's definitely a bug.

Thanks in part to John Wolff's post, i went into my iPhone-->Settings-->iBooks and clicked OFF 'Sync Collections' and 'Sync Bookmarks', I also--and this is key--clicked off 'See Purchases'--or something very close to it. This removed that new default category 'Purchased Books' from my iBooks on my phone (4S).

Then i went to iTunes and connected my phone, clicked on 'Summary' and clicked OFF 'Sync with this phone over WiFi'. Thank you, Mr. Wolff.

Then i went into my iBooks on my phone and clicked on the Store, then on 'Purchased', and there they all were! I selected and downloaded quickly all the books that USED to be in my collections but had disappeared (unlike when I did this from the 'Purchased Books' bookshelf, I could download several at once). Interestingly enough, some went obediently back into the collections i created (young adult, for example, and 'Laugh with Leacock' collections) while others just downloaded into the 'books' default bookshelf.

We'll see if they STAY!

Thanks to both John Wolfe and dalywhitter for your help!!!!!!!! I did what you both said and have now spent the last hour rearranging my books for that bazillionth time.......I hope this does it!!!!!!

Tried everything, switching of the show purchased items in iBook setting on iPad etc, switched off the sync in iTunes etc and nothing worked. It actually made things worse with dozens of multiple copies of each purchased book showing after I turned the settings back on.
In the end I deleted iBook app from my iPad and then reinstalled it.The bug is gone and iBooks is working as expected.

I think you are onto something as I noticed that the problem was occurring mostly after trying to read off my iPhone...99% of my reading is off the iPad. SO, in addition to doing what John Wolfe and dalywhittaker have suggested, I also took the app off my phone. It's hard on my old eyes, so I'm probably better off not trying to read from it any ways!!!!!!!

THANKS SO MUCH from all of you!,,

I just checked 24 hours later and all my books are still there. In the last few months whenever I opened iBooks on my phone the 'Edit' button would blink several times as the phone synced with iTunes, and then one or more books would disappear. This time the phone couldn't sync...And all my downloaded books are still there.

Thanks for you suggestions but it doesn't appear to have been a syncing problem for me but rather a bug in the iBook app. Since removal and reinstall of iBooks it is now working as expected and syncing over multiple iPads and iPhone without any glitches. Created categories are syncing across all units and holding all downloaded purchased items as expected.

I too have been having the same problem and can now report that with OS X Mavericks that the problem extends into iBooks for Mac. When I opened iBooks for Mac the first time, all of my books were in their proper collections and all of them were in the cloud. I was overjoyed but it was short lived. Within a few minutes, books started vanishing and now iBooks on my Mac looks just like the broken iBooks on my iPad and iPhone. I've tried to repopulate the collections again from Purchased Books on the Mac version and for a few minutes they showed up correctly on my iPad. Then everything vanished again.

Very, very frustrating...

I am so tired of apple doing this they think is better for me

This is the second time I have my personal pdf files dissapear !!

It is not right that i have to waste all my time and energy to redo my books and files THE WAY I WANT because it my device I paid for it !

I now do NOT open anything else on ibooks instead I open them in Dropbox and things stay there the way. I want and where I want for as long as I want

After may years using only apple devices , macbook, iphone and ipad I am beginning to consider ANDROID devices

This is very frustrating and irritating

My problem is all of my books are loaded from my personal cds. Everyone is now in the cloud and not accessible to my classic iPod. Why classic? I have over 32gb of books right now and needed the largest drive offered.

I cannot reinstall the books using my PC because they go back into the cloud. And there, they are not available or only partially available. I have had to go to a separate laptop to install the books and load back to my iPod, something I did not want to do.

I feel Apple has made an error in their iCloud and is not willing to admit the problem. If I could, I would stop using all Apple devices.

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.