If it is an official Amazon file, containing a mobi-asin and was never converted (it won't have the "personal" banner) the thumbnail MUST be sent to it! calibre will do this automatically.
I have noticed if this file is a .mobi, the Kindle won't recognize a change until you delete and re-add the book. I keep a rsync backup so it is easy to restore everything.
For anything that will have the personal banner, your Kindle will autogenerate a cover when it sees there isn't one already.
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