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Generate Cover only updates the cover in Calibre's database. It doesn't change any ebook format.
By default, Calibre's Convert and Send to Device both update the metadata inside the ebook file, including cover, when run. As far as I know, anyway. It's possible that the defaults have changed, or you have changed the settings without realizing it.
Calibre's Polish can be used to update the cover in ebook files in place, vs when they are converted for sent.
FYI, azw3 is a newer and 'better' format than mobi for Kindle. I would recommend using it instead of mobi. I've been using it for years.
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