Another thing to note: ADE puts books in a different place than calibre. This can result in having two copies of the book on your device.
To help mitigate this problem, ensure that the Sony plugin preference "Search for books in all folders" is checked. You find this preference at preferences -> plugins -> device interface plugins -> sony. Once that preference is set, then use the device view to delete all the copies of the book. Then as itimpi said, ensure that the newly-downloaded epub is in calibre (replace the epub existing format using edit metadata), and then send the book to the device.
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