If you've deleted cover.jpg you have done the same kind of damage that deleting a book format from your library folder does. It puts calibre's database "out of sync" with the physical folders. Thats why there are the big warning all over the place about not digging around in or touching anything inside calibre's library folder. Run Library maintenance to repair the damage.
*Nothing* looks at the cover image inside the book formats. QC cover checks are all based around whatever cover.jpg is associated with books in your library, and that can and often will differ from any cover embedded inside the ebook formats itself unless you do conversions or use Modify ePub.
Your other comment is nothing to do with this plugin. If you want to remove jackets safely, use Modify ePub.