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WHen I was playing around with a Kobo Touch and had a similar problem I deleted the two calibre files (don't remember their names, but they had something with "calibre" in the extension as I remember it, and they showed up nicely in my regular file explorer), deleted the book file and reloaded it, but didn't involve Calibre that time.
This was not using the latest firmware, but probably 1 or 2 versions back.
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