This free and open source software under the name of
Ant Renamer (FossHub download page
here) made it easy, fast and painless for me to bulk-rename dozens of .kepub.epub files to .kepub
I only had to throw all the .kepub.epub files in the program, then Actions > Change extension > [leave the field 'Replace extension with' completely blank] > GO - and the files got all renamed to .kepub in an instant.
(-- Even if there's an 'Undo' feature in the program, please note that Ant Renamer will rename the files in the original directory by default, so make a backup of the original files in case you are just experimenting --)
Afterwards I added the resulting .kepub files to Calibre and sent them to Kobo: they are properly formatted, as expected.
Thanks again for the insights and for the very useful help! Learning curve is getting less steep by the day!