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The cover image displayed in calibre is not the image inside of the ebook, but a separate JPEG file associated with the ebook. Initially, this JPEG is the same as the cover image in the ebook, if it had one. When you change the image in calibre, only this external JPEG is changed. The cover embedded in the book is not changed.
You can have calibre replace the cover image in the book with the new one calibre is using, but you must do the manually. With ePub and AZW3 there are functions or plugins to do this easily (somebody step in and specify which, please, as I'm not where I can run calibre and get the correct steps). Converting a book, even converting to the same format as the original, will also replace the embedded cover image with the new one. With some formats, like classic MOBI, this is the only way to change the embedded cover image.
Once the embedded cover image is updated you can reload the ebooks onto you device and you will see the new covers.
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