Try this:
before unplugging the device, copy the folder "[userstore]\system\thumbnails\" to a backup folder, e.g. "[userstore]\system\thumbnails.bak\"
Unplug. Let the Kindle do it's weird thing...
Reconnect your Kindle, delete the first folder and replace it with the backup.
@blaenk reported that this works, the Kindle will only override your cover thumbnail when the ebook itself is added/updated.
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