The driver knows to send a kepub to the device without adding the spans. But, adding a book with the extension .kepub.epub to calibre will add it as an epub. The driver will try to add the spans. I don't know what will happen. If you want to use those books, drop the .epub from the name and add that to calibre. Then, it will be treated as a kepub.
If you do this, you should also install the Kepub Metadata Reader and Kepub Metadata Writer plugins.
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