I tested some more and what I discovered is very surprising.
If I re-send the book through Calibre (so that it re-sends the cover art to the thumbnails directory), I do see that Calibre puts the correct cover art file in the thumbnails directory. I copy and paste that file to a folder on my computer as a backup. I then eject the kindle and it shows for a split second before being replaced by the downloaded one.
I then reconnect the kindle and it shows the newly downloaded one in the thumbnails directory instead of the one that Calibre sent, so yeah it was overwritten.
If I then _manually_ place the backup I made earlier of the file that Calibre placed, replacing/overwriting the one that kindle downloaded (which itself overwrote the original one that Calibre sent), then I eject, _then_ the kindle STOPS downloading and overwriting it!
It's very weird as I can't imagine what is different from Calibre putting it there and my putting it there manually, but the effect is reproducible: if Calibre sends it, the kindle downloads and overwrites the cover art that Calibre sent. If I place the cover art there manually (the same exact file, same name etc.) then the kindle doesn't overwrite it.
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