What you're doing wrong is trying to work with files, not books.
Calibre manages books; it's a level of abstraction on top of files the way files are a level of abstraction on top of the disc structure. You don't worry about what tracks and sectors represent your files; likewise, with calibre, you don't worry about what files represent your books.
The longer explanation is here:
https://www.mobileread.com/forums/showthread.php?t=85232