Click the Library dropdown icon (caron) | "Library Maintenance" | "Check Library"
Click "Yes" if you get the message: "Found no errors in your calibre library database Do you want calibre to check if the files in your library match the information in the database?"
Also, according to calibre recommended guidelines,
never use Windows explorer to edit anything in your calibre library directory.
For the empty book entries, you could have done a search for "formats:false" and deleted them that way.
I have a related post on my experience with merging/deduping calibre libraries that mentions using the "Duplicate Finder" plugin. See here:
https://www.mobileread.com/forums/sho...16&postcount=4