[Sirtel]

It seems strange to you because you see Calibre as a converter, but Calibre is first and foremost a library manager - that is its main purpose. And you're supposed to work with your files via the GUI, not directly.

Save to Disk is meant for working with/manipulating the files themselves - it saves them outside Calibre, so you can do whatever you want with them without messing up the library structure.

There have been many posters with similar problems and questions, who only used Calibre for converting and therefore didn't understand why Calibre has such a rigid way with the files in the library. They thought Calibre was first and foremost a converter. But actually Calibre was created as a library managing tool and many decisions about its basic functioning reflect that. Converting is just one of its features, not its raison d'être.