If you use calibre and convert a kepub, you will screw it up. The only way to fix a kepub is to remove the DRM (if there is any) and use Calibre's editor to edit the CSS to fix the paragraph spaces.
The following URL is where you should go to get the plug-ins for Calibre to remove DRM and to get help/learn how to use the plug-ins.
https://apprenticealf.wordpress.com/