Sometimes, at least for my Sony, I have noticed the metadata not updating the first time I plug it into Calibre. When I eject and then reconnect, the next time the metadata is correct. Not sure if that would be an issue with a Kindle. (I use automatic metadata management, which takes quite a while after plugging in one of my Sonys, but hardly any time with the Paperwhite. Though the Sony's have hundreds more books on them. Thousands more).
Anne, Mom to 4 kids & 4 Parrots.