You hit a caching issue. Replacing the book like that isn't really something that Kobo supports. In fact, if you update a book manually, the device will remove all the information it knows about the book and then add it as a new book. Which means you lose the reading status, collections and any annotations. The KoboTouch driver in calibre cheats and tries to make the device not think that the book has been replaced. But, it means that the device does not know to generate a new cover. It will happen eventually such as after several other books have been opened. But, restarting the device is the quickest way.
I have mentioned this to Kobo, but I'm not surprised it hasn't been fixed as it only happens because of the cheat.
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