I think "user_none" was suggesting you navigate in Calibri to one of the books that is un find able in Explorer.exe. Then rclick and select "open containing folder"
Then you should see it in Explorer.exe along with the path etc, you may then be able to work out what happened.
But forgive me if thats of no help, as to be honest I'm a bit confused with which book is hidden or not
I always copy and check the files too, then if theres problems I use a verification app to redo the copy. If there are any issues I grab my backup. failing that I get my other back up from dropbox. If all else fails I pop in my clone drive... lol
Hope you can sort it out.