So, last month I decided to enable iCloud for Books in order to transfer all 400+ of my PDFs to my iPad automatically. However, in doing so, all of my PDFs were deleted from my iPhone!
I did the whole "turn it off and on again" and re-enabled iCloud for iBooks, and I did get half of them back (only half because my iCloud ran out of storage when syncing to my books). I'm not too bummed about that, for personal reasons (one being that even I'm not sure what exactly got deleted when I have so many).
My main issue is this- iCloud won't allow me to store my PDFs locally on my iPhone anymore. If I download a few PDFs back onto Books (using the download button in iBooks) and disable iCloud, every PDF (re-downloaded or not) in Books disappears again! I have almost 400 PDFs saved to iCloud right now, and it's already been proven that re-downloading each PDF individually and disabling iCloud won't fix this.
How do I get Books to allow my PDFs to be stored locally on my iPhone again?? Again, disabling iCloud sync just removes all of the PDFs from Books, even after re-downloading.
I am using an Apple iPhone 6S+, with an 13.3.1 OS, and I have about 13GB of storage still free.