Q: Since I updated to IOS 9.3.1 my iBooks PDF documents are uploaded to the Cloud so that they can be shared on multiple devices, however when I rename a PDF document it reverts back to the original name every time iBooks is refreshed.

I sure hope they fix this soon.  It's distressing to have discovered that my renamed PDFs are back to the hard-to-identify filenames given them by their originators.

Same thing here. Change the title of the PDF on my Mac (OS X 10.11.4) and the title stubbornly refuses to update on iPhone or iPad (9.3.1). I even tried deleting the pdf from iBooks on the Mac and then adding back in. Still the same name. Same thing is true for authors. It seems that the metadata is not being updated.

Good news, at least, is that all my pdfs are in iCloud for iBooks at least.

I tried turning off syncing but that didn't change anything.  And the PDFs I've made from screenshots are all named "untitled" now, instead of the phrases I used to identify them -- for instance, "bus route to city hall" or the like.  Having dozens of PDFs named "untitled" in iCloud for iBooks is useless to me.

I Have the exact same problem. Spoke with several Apple support techs over the phone with on luck. Went into to the Apple Store and the Rep was dumbfounded when he was unable to rename his PDFs in Ibooks. They kept reverting back to there original name once they were refreshed. He concluded that it was a software issue that Apple we need to send an update to fix. The only solution would be to download a third party APP such as PDF Expert and email the files from your IBooks to yourself then save them to the third party PDF APP. I have 400 PDFs that have all been virtually renamed to an unrecognizable names. Before I buy the App and spend hours downloading my files Via email, I want to see if Apple has identified the problem and is working toward a solution. Very frustrating to say the least. They really screwed the pooch on this update for those of us who rely on our files in IBooks.

I also have hundreds of PDFs.  I was already thinking of leaving the Apple domain for a Microsoft tablet because of the inability to mass export from iBooks, but if Apple doesn't fix this renaming problem, I'll be a CONFIRMED ex-iPad user! 

I hear using surface is a blast, keep us updated how you like it.

I too will be an ex-iPad user if the problem is not corrected.

My husband keeps his PDF in Goodreader, which he prefers over iBooks for PDFs. You might give it a look

Why are you e-mailing yourself pdfs from iBooks? Seems inefficient.  If you have a Mac, they can be accessed directly in ~/Library/Mobile Documents/iCloud~com~apple~iBooks/Documents For Windows, I would presume there is a equivalent location, but I do not know what it might be offhand.

I can't answer for Rstraut about his/her reasons for e-mailing PDFs one-by-one, but as far as I know, that is a only way to do it if one is normally a PC user.  There have been complaints in the Apple support forum for years about the inability to mass-export our PDFs.

You are probably better off moving them to something like Goodreader then. Goodreader has file transfer and synching abilities, among it's many other abilities. It works with iCloud, but also allows you to transfer files using sftp etc.

Looking into the filesystem for iBooks, I see that the files are renamed, it's just that the metadata is not updated. Nothing seems to force iBooks to update the metadata when you use iBooks itself to rename/rename author. I managed to get around this using Calibre, which is an epub tool. It allows the metadata file (.opf was it?) to be created and then the complete folder imported into iBooks with the updated file name etc.

I do not recommend doing updates this way if you have a lot of pdfs. Also I do not know how one would do this on a PC. Best thing to do is to submit a bug report to Apple. It's pretty clear to me this is a bug that was introduced in a recent iOS update.

I have the same problem, but the funny thing is I was able to rename some files but not others!  Very annoying!

Were the ones you could rename dated from before the new IOS update?

I believe they were but not sure.

I also found the link above for direct iBooks access, but I run Parallels with Windows 10 on El Capitan.  The only way I can access my 1500 or so iBook PDF's is through Windows, and it only just started working too - sort of.  But at least now I have full access where I can add, rename and delete anything I want.

But what I can't do is map to it. I have turned off hidden files and I can follow the path as far as the Mobile Documents folder, but no further - see below.  Does anyone know how to map to it on the Mac.?   Ideally I'd like to sync it with our corporate folders on OneDrive.

It looks like its a folder inside iCloud, but when I click onto it its not there.  Three are showing, the rest are hidden - but not iBooks. 

All in all however, while the idea of iBooks in iCloud is great, the implementation is a royal mitigated disaster.  And it seems I'm not alone - https://tidbits.com/article/16378

Anyhow, wait another version or two and I'm sure it will pickup  (remember Apple Maps . . .    -:)