Title is self-explenatory. I really didn't do anything special, all epubs, PDFs etc are gone. I restarted the computer, same result. I have only used it from my MacBook, no iPhone, iPad or anything else.

I checked time machine at username>library>contents>com.apple.BKAgentService>data>documents>ibooks>books and weirdly I could only find books starting from many months ago and not sooner. For at least the last 3-4 backups this folder was empty, which is insane as I use iBooks every day and that definitely wasn't the case until now.

I restored these books, copy and pasted them at the present time username>library>contents>com.apple.BKAgentService>data>documents>ibooks>books folder but to no avail.

This is so weird as we're talking about hundreds of books!

Is there a standard dumb thing I may have unknowingly done for this to occur? What else can I try to resolve this?