Calibre is great once you get the hang of the interface. The one thing I haven't yet figured out is how to stop it from butchering Kobo (kepub) ebooks downloaded from Standard Ebooks:
"Important: Don’t use Calibre to transfer the kepub file! Calibre will apply its own conversion on top of our own conversion, making for strange results" from https://standardebooks.org/help/how-to-use-our-ebooks
Thanks, I've found the Standard Ebooks (both kepubs and epubs) quite good and would recommend them if you're looking for something in the public domain. The downside is that their kepubs did not play well with Calibre.
By default Calibre didn't recognize Standard Ebook kepub files as anything other than a regular epub which caused it to reformat it (poorly) when sending to a Kobo eReader. It also prevented me from storing both the kepub and epub versions in my library.
There may be a better way but the workaround I use for now is to rename the kepub book files from .kepub.epub to .kepub which the Kobo eReader handles equally well. The downsides are that I have to remember to explicitly send the kepub format when I'm sending to a Kobo and I occasionally get notifications that there are duplicate book files in my library.
"Important: Don’t use Calibre to transfer the kepub file! Calibre will apply its own conversion on top of our own conversion, making for strange results" from https://standardebooks.org/help/how-to-use-our-ebooks