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I can tell you how I do it with an epub using sigil, after which converting it to azw3 will preserve the cover properly. There's probably a less intensive way to do it entirely with calibre. In sigil add the cover image to the images folder, then right click on it and select cover image, then in the tools menu at the top select add cover and in the window that comes up select the cover image from the previous step. Save and quit. Now you can convert it to azw3.
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