[TechniSol]

I'm not sure Calibre is intended to delete empty shelves as they are maintained by Kobo's servers, though it can create them. I think you can just delete them from the collections page, and maybe then sync to get them off Kobo's server. You realize you need to transfer the books from Calibre to the reader, disconnect, let it process them and re-connect with calibre running to get the shelves built on the reader. It won't build the shelves until after the books are processed into the ereader's database and you reconnect. I think it builds the shelves right after it scans and sees what books are on the reader, as I recall.

I'd do the update and then mess with one thing at a time until I was satisfied with results. 3.3.0 seems pretty good to me.

Behaving like a kepub, could you have or have had a kepub version of the epub in question and it still thinks it's a kepub due to something in the database once you've synced with kobo? I've had my Glo and Touch tell me I couldn't read a book because it was protected by DRM and I hadn't set up the account info for Adobe DRM -on a sideloaded file with no DRM... I believe a power on-off or possibly signing out and back in to rebuild the database fixed it.