[itimpi]

If you do conversion using the Calibre Command line (CLI) tools then you have explicit control over where files are placed. If you do it via the GUI then Calibre assumes it is managing the books and keeps them in its database.

It sounds as if you are going into the underlying file structure of the Calibre library to get at the converted books? This is strongly discouraged (think of it as a black box you should not peek into). Instead you should get books out of Calibre using its Save to Disk facility. In the Calibre Preferences you can customise the template for the folder/file names to be generated when using Save to Disk this may suit you better as it would allow you to tell Calibre both the folder structure and filename format to be used when exporting the books.