At the moment, there isn't a way to do it. The Kobo firmware loads the ToC into the database when it is first imported. If you replace the book, the firmwares default behaviour is to remove the book from the database and import the updated book as a new book. Which means you lose the reading status. The KoboTouch driver has a cheat so that this is not done. But, it means the ToC is not updated.
I have been, slowly, working on a solution to this. It will be added to my Kobo Utilities plugin. Hopefully I will be able to return to this soon.
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