Fun fact: when Nickel fails to sideload a file, you don't need to channel your inner Hercules Poirot to figure out which ones didn't make the cut, nickel will helpfully log that for you!
Code:
logread | grep "This epub file is bad"
will do the trick.
So, yeah, you need shell access.

.
This may have been there for a while, but I've only ever setup a grand total of *two* Kobo devices, so

.
(Yes, I'm a crazy person who stores kepub files in his Calibre library. There's a reason. It even makes some kind of sense!

).