exactly the same for me. This is the worst ever released application from Apple IMHO.
All my well kept and organised books and pdf's are now in disorder. Lost their category settings, their author setting and on top of all can't be edited in iBooks anymore and any further. No chance to edit wrong typings and to fill missing information (eg. authors, categories, ...).
I used to organise my papers (mostly PDF's) in iTunes like a document manager, the way I needed them on my various iOS devices and used them for work. I had groupings for my books like computing - networks, computing - guides, computing - iOS, computing - scripting, etc. .... now all is gone and lost. How am I supposed to organise over 1300 papers without any editing possibility (only sections can be assigned, no categories can be, neither can any information be edited/changed/corrected?
And on top of that all: HOW DO I BACKUP / RESTORE MY BOOKS from now on?
The books and PDF's are moved from the iTunes Library, where they were accessible and editable and where I could backup my whole media library on external NAS and storage. How will I get back my books/PDFs in the future if I setup my Mac Pro again from scratch or in case of a disaster (eg. failing disk)? Am I forced to use TimeMachine here?
There is no way to define by myselfs the place where the iBooks are stored on my system. No, they are all moved to some well hidden place into the users-library filling up my (until iBooks/Mavericks) system only SSD hard drive with hidden books. Is this the new strategy of Apple to try to make me under-age?
No editing, very limited organizing, no possibilty to define it's own storage-location, no backup/restore (no export/archive like in most other application like calender, addressbook, mail, etc. ....) what the **** is that?
I like most of Mavericks new additions but this here with iBooks is a mess and complete drawback for a user that liked to read his books on his iOS devices and was well organized.
And to be honest, I seriously consider to migrate back to OS X Mountain Lion just because of this ridiculous implementation of iBooks!