The following actions might produce some new information:
- Move the library to a new location using the new Calibre feature. Orphan stuff should be left behind in the old directory. Is there anything there?
- Use the Calibre Catalog feature to produce a Catalog in CSV format with all output fields selected. This could be opened with Excel (or something) and sorted every whichway to look for duplicates.
(Apologies if either of the above has already been tried. I've lost track.)
However, if it was me I would be doing as Starson suggested and start a new library with one book.
Make change - peek under skirt. Close any open peeking files.
Make another change - peek under skirt. Close any open peeking files.
etc... etc...
When does the first problem occur.