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Ah, but you had one book in two different formats on the device.
All of the files that a Kindle generates when a book is put on user store are not deleted with the book.
So it is probably just a matter of confusion (either software or human) -
Take both of the copies of the book off the device -
Browse the directory tree visible over USB for things that seem related (the names are usually a give-away) and delete those also.
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