You went
under the skirts and made changes
Calibre does not know about your changes.
You have damaged your Database (files are part of the DB, even tough they are in the file system.) Stay OUT (unless you absolutely know your activity is safe. Rule 1:Change only the Insides of the file. There is no Rule 2.
)
Calibre can delete Single formats (at least 8.37 will do it correctly, again)