Originally Posted by kovidgoyal
The only way I know of for what you describe to happen is if the book id in the opf files dont match book id in the directory names. I have no idea how that happened unless you changed the directory names outside calibre.
The only thing you can do at that point is create a new library and add the books to it from the old library folder using add books from subdirectory, one book per folder.
Why doesn't check library show that (i.e. the book id in the opf files dont match book id in the directory names) up?