Firstly, the ToC update in the plugin shouldn't let you update purchased kepubs. It shows the book as having a not supported format. I'm not sure what happens if you actually try to do the ToC update.
It would be possible to update the database and set the word counts to -1. I would expect that would trigger the word count calculation like for a sideloaded book.
The other way I have fixed some issues is to archive the book. That removes it and all details from the device. Then you have to go to the library on the Kobo site and restore it from the archive. I'd be surprised if that doesn't solve it, but, I'm also surprised that the simple removal and download didn't.
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