Most of iTunes/Books library gone—how to fix?

[KevMA]

I have a bunch of books and PDF files on my iPad (as well as these having annotations/bookmarks). For some reason, 4/5 of these disappeared from both iTunes and from the Books app. I'm guessing syncing will delete the 4/5 of the books/annotations that are currently on my iPad, so I haven't done that.

How do I fix this? How do I get the disappeared files back to iTunes and Books?

 

[pika2000]

You can try emailing those PDFs to yourself or uploading them to cloud services like google drive or Dropbox first.

 

[KevMA]

I got it to work by saving a few books that had a bunch of highlights using the iMazing trial (5 books maximum), making sure all the iBooks and iCloud syncing settings were on, hard-rebooting both the iPad and laptop, deleting everything (make sure you have the original files), re-uploading to the Books app, and then syncing everything in iTunes (worst app UX ever, Apple). Sadly, the highlights/bookmarks aren't syncing between OS X and iOS.