The Kobo devices don't support syncing info about sideloaded books, only kepubs purchased from Kobo.
For the covers, the Kobo devices read sideloaded books the first time they are seen for metadata. And then they generate a cover the first time it is needed. If you sideload a new copy of the book after the covers images are generated, new covers are not regenerated.
But, if you send the books again from calibre, the driver will remove the generated cover images on the device. This will force the covers to be regenerated from the new copy of the book. You can also set options in the driver to get calibre to create the cover images. This can result in better images.
There is one catch with the above. If the book is one of the books on the home screen, the device caches the cover images in memory. They don't get replaced with the latest version until the books leave the home screen or the device is restarted.
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