Weird. I've bought hundreds of books from Kobo, but NEVER use the kepubs; so I have hundreds of DRM-disinfected, sideloaded epubs on my reader, for which there is a kepub equivalent in my account, but I don't have your problem. The only difference I can see is that I don't use Calibre to sideload my books but simple drag-and-drop. Have you tried that?
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