[Adoby]

Orphan books / database entries.

This can happen when you move a calibre library between different operating systems and/or different filesystems that handle character cases different. In Linux (and I assume Mac) the book titles "This Is A Title" and "This is a Title" specify different books. In Windows they specify the same book.

Orphan files / database entries can also appear if you restore a library from backup or copy an old library to the folder of a new library. Or perhaps(?) if some anti virus or cloud backup program kept files locked when you updated metadata. A mix-up.

One way to handle this can be to create a new empty library, with the same structure as the old library, and then use Calibre to MOVE (= copy and delete after copy) all books in the old library to the new library. Note errors and afterwards look in the old library folder to see if there are some orphan folders / books left. If that is the case you can manually add those books to the new library. Hopefully that fix the problem for you.