@clarkekent I decided some time ago that I would only ever download the epub version of Kobo books (into Sony Reader) and then import them into Calibre, and your story is exactly the reason why.
When I buy, or download a free ebook, I want to know that I'm going to be able to keep it for ever, or whatever length of time I determine, and so Calibre is the way I ensure that.
I couldn't even tell you whether the original copies of Kobo's Kepubs are still in my Kobo Desktop, because I don't need to open it. I started a dummy Kobo account and use that as the sync for my Glo.
I don't buy anything with the dummy account or use it for any other reason than to sync updated firmware.