Note that in Calibre, when you try to Send books to your kobo, Calibre will first convert the epub books (using kepub output plugin) to .kepub.epub in temporary directory in you PC and then send the .kepub.epub file to your kobo, after that, Calibre will delete the temporary directory.
@geek1011 is developing kepubify output plugin for Calibre (
https://www.mobileread.com/forums/sh...d.php?t=312308) to replace the kepub output plugin, it is still in early development, but you can just try it or just wait.
Currently kepubify doesn't work with Calibre, but you can try to convert all your epub files to .kepub.epub files using kepubify, and load them into Calibre and them send the .kepub.epub files to Kobo, but I never try it, I'm not sure it will work or not.