@
lumpynose - below you see a very basic Book. I created the cover with metadata edit Generate Cover. Update metadata in calibre does
not touch the book files - this is a deliberate design decision. Hence the cover is not in the epub.
When I run Modify with
Insert or replace cover checked I get a book with a cover page and ONE image file -- cover.jpeg.
When calibre sends books to devices or saves them to disk it provides the option to send/save with the current metadata embedded in the format sent - including covers. Hence for many calibre users there is no need to update the library copy.
I know less that nothing about Kobo; so, I'll let others address the issues related to that particular device
BR