Kobo books downloaded by the kobo desktop have always been kepubs, haven't they? It's just that most of them also offered an adobe download, too. Kepubs uses kobo's own DRM scheme, and therefore avoids a license fee to adobe, and can potentially be more secure.
The problem seems to be that some now don't offer the adobe option. I have yet to encounter this. The first time I am unable to download a book I have bought will probably be the last time I deal with kobo.
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