You can NOT use (keep existing) books outside Calibre as THE Library and still have Calibre show them.
Do spend some time reading the official FAQ and that should save your hair.
https://manual.calibre-ebook.com/faq.html
Calibre Builds a DB of Metadata AND where it put the book, that is kept With the books (another reason to stay out of that folder. resist changing anything inside. Only Calibre should make the chandes)