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Firstly, if you send a kepub to a Kobo device, the extension is changed to ".kepub.epub". That is how the device recognizes a sideloaded kepub. So, that is what you wanted to do.
The only way I can think of to delete them via calibre is a bit clumsy. It is OK for a couple of books, but, not for a lot. When doing this in bulk, you are better to remove the books first, and then send the replacements.
When the device is connected, calibre will show which book have multiple copies on the device. You can select them and press the delete button. You will then be prompted to chose where to delete them from. Choose the device. A list of all the books will be shown. They will all be selected and will have the format "epub". You will need to look at the file name to see which are epubs and which are kepubs. Unselect the ones you want to keep, probably the kepubs, and press the OK button to do the actual delete.
As I said, clumsy. I'd probably just delete them from the device while it is connected using a search on the drive. Then disconnect and the device will cleanup the database and the cover images.
The other problem with all this is that you will lose the reading status of the books. The status is kept for the copy. If you put a another copy on the device with a different file name, it is treated as a completely different book and status is tracked for it separately. If you want to store the status, my Kobo Utilities plugin has function to fetch the reading status from the device, and later restore it. Or just set the status for selected books.
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