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mobi doesn't support covers as a metadata type, so it will be added as a new first page in the file but send to device will NOT update it.
azw3 is the newer version of mobi, and supports more cool stuff.
If you just want to see the cover in cover view on the home screen, then for books with an amazon ASIN (meaning it came from amazon, or you added it manually with special programs -- calibre will always use a UUID for this field if converting) calibre will upload a thumbnail to your device with the book. Thumbnails are located at %KindleDrive%\system\thumbnails\ and have the naming format "thumbnail_{insert books ASIN here}_EBOK_portrait.jpg" if from amazon.
Since these are sideloaded however, things are trickier. The Kindle will try to extract the cover, by assuming the first picture in the book is the cover, and fail, and the "thumbnail_{six random letters}.jpg" of sideloaded books will probably never get created. It is possible, however, that it will create a 0 KB file of that name, and by replacing it, you can give trick your Kindle into giving it a cover. But you'd have to guess which is which.
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