COPY to Library is NOT an OS function.
It is a right-click (context menu) option.
Creating the Library (step 1) made the metadata.db (0 books)
Copy to Library, moves the books and make entries as it goes.
Delete after copy removes folders that transfer
What is left, is your problem books
RULE #1: Never use the OS to make adjustments

to any file or folder in the Library. Calibre does everything needed from the GUI or CLI tools and keeps the DB in sync with reeality