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There's two KePub plugins, a driver plugin and a conversion plugin. If you use the conversion plugin, calibre stores the book as a separate format in its database. If you use the driver, the book is converted as it is being sent to the Kobo device and the KePub result is not stored in calibre. The driver is aware of the conversion plugin, so if you convert a book to KePub you can send the KePub format using the driver and it won't re-do the conversion.
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