Originally Posted by John F
I'm not sure this is correct? I believe that Kobo shelves are stored in a database on the device (and maybe a Kobo server, if you're syncing).
You may be right, John. I'm not sure how the Shelf data is passed from Calibre to the Kobo database. I thought it was via the epub metadata but I suppose it's possible that the Calibre driver manipulates the Kobo database directly. As the OP is only using sideloaded epubs I don't think the Kobo servers are involved.