Funny how this seems to be cropping up for some of us kepub addicts.
I experienced this today when converting some epubs.
Besides the tips mentioned previously, I still had issues converting to kepub. I finally discovered that I was missing the kepub output plugin. Somehow it got uninstalled as I've been converting to kepub for years. And I did not upgrade to a more recent calibre version (on 3.22.1). I may have inadvertently uninstalled it when mucking around with trying to remove Nook DRM.
For those who still may experiencing issues with converting to kepub, I did the following ...
In Calibre:
Plugins > Conversion Output Plugins > Get new plugins button > Filter by name: kepub
Restart calibre after installing and you should be able to convert to kepub.
