Change the extension to just ".kepub" before adding the book to your library. Then calibre will add the book as a kepub. The only thing that will treat a book with the name ".kepub.epub" as anything other than an epub are Kobo ereaders. And as they are generated from epubs using plugins in calibre or kepubify, you are generally better off just using the original epub.
But, if you are doing this, you will also want to install the Kepub Metadata reader and writer plugins.
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