Restore ebooks (PDF) from iTunes backup?

Upon opening iBooks.app on my clean Mavericks install, I noticed that all my ebooks from other sources than the iBooks Store were missing. Of course, they're not saved in iCloud. So I wanted to restore them from the Music/iTunes Media/Books folder of my Time Machine backup. On my backup disk, there was no Music folder.. I forgot I had excluded it from the backup. I wanted to save space, and I'm using iTunes Match anyway, but I hadn't thought about the books.

All the books and PDFs were still on my iOS devices, which started syncing with iTunes immediately and deleted all books in the process instead of transferring them to my Mac.

Finally I had a look at the MobileSync folder on the backup disk. The backup seems to be some kind of database. I used grep to search for a few unique terms from my books in the binaries, and they are indeed in there, somewhere.

I've tried to copy the folder to my Mac so I can look at the backup with iExplorer, but it doesn't show any books. Which app can I use to simply extract the books from the backups?

There is an application called iPhone Backup Extractor that will help you extract data from an iPhone backup. it will convert the files you see in the backup with randomly generated names to things you will recognise.

When you run the application and identify the backup you want it to use it'll give you a list of all the application data contained within the backup. BTW you'll need to move the backup folder so its sitting at /Users/YOURUSERNAME/Library/Application Support/MobileSync/Backup/LONG_GIBBERISH_STRING for iPhone Backup Extractor to find it.

I'm not 100% certain where Apple stores books/documents that haven't been purchased but my guess would be within either "com.apple.iBooks" or "iOS Files".