[GeoffR]

If you sync the books to your device AND download a copy from the website to add to Calibre, then as long as they have the same title and author, the ones that are on the device will match the copy in Calibre.

The books on the device will not be treated as sideloaded books, i.e. they will still be KePubs even though the copy in Calibre is an ePub, and they will still sync etc., but you will be able to use Calibre to change the covers and other metadata in the same way as you can for sideloaded books.

I do this for all my synced KePub books, it is very useful to be able to correct the metadata, add series information, etc. (Edit: by using the Kobo Utilities plugin.)

You can also just create a dummy book in Calibre, i.e. create a book entry without adding any format, and use that to match the book on the device instead of downloading an actual copy of the book.