Books mysteriously gone missing

Some of the books (not purchased through iBooks store ) added to iBooks Library would disappear from the book shelf after quit and relaunch iBooks app on Mac.

And if I try to reimport these books back into iBooks Library, an prompt would come up asking if I want to replace them as shown below.

If I choose Replace, the books would reappear, but only to disappear again from the shelf after I quit and relaunch iBooks app.

This is not a new issue, it is an ancient unresolved issue with first appearance dating back at least 2 years.

the temporary workaround suggested in Re: iBooks in Mavericks lost 700 books

1. first drag all the problematic files out of the folder [ ~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books ]

2. import them into Calibre, then use "save file to disk" to save the ePub files into another folder

3. import the newly exported files back into iBooks, it should work now.

But this workaround has its shortcomings: all the annotations and categorisation associated with these books will be gone. That is going to be a huge pain in the *** if you have accumulated a large collection of ebooks.

this problem has forced many users downgraded their system back to Mountain Lion, which is probably the last known version with a truly usable iBooks app.

Hopefully Apple can fix these kind of glitches eventually since Apple is so keen in Education!

"soon" is an adverb definitely out of the question in the current context.

OS X El Capitan version 10.11.3 (15D21) which comes with iBooks version 1.4