I suspect it's a database flag. I've taken a copy of my Glo database at 2.8.1 and the Aura database at 2.9.0, and made sure the Aura database had KePubs from Kobo in it, so hopefully there's something I can do. It may just take a while to figure anything out
While I don't like that Kobo did this, I keep saying that this plugin enables accessing a renderer that Kobo doesn't want us to access, using files the renderer was never intended to handle converted to a (likely) incomplete and inaccurate facsimile of the native Kobo format, all by adding books in a way Kobo has no obligation to support. For now, I'll just be happy that they didn't break KePub sideloading entirely