That is incredibly odd, and I don't believe anyone has ever seen that before!
I know on my Kindle Touch, I sideload all my Amazon-bought books, and calibre adds the covers which sometimes are different than the official ones, but anyway are in color, so I know which ones calibre sent.
The Kindle has never overwritten them once a thumbnail exists.
The only thing I can think of is that Amazon changed something in the newest firmware -- although I would think other people would notice it as well!
And according to that logic, when you resend the book with calibre, the Kindle notices the timestamp changed and therefore the book is different -- and redownloads the cover art?
Some factoids for you
:
The random UUID thumbnail is what you see when calibre creates embeds a random UUID in the exth 113 field -- that is why I don't like calling it the ASIN field, because it only sometimes is.
system files/folders are different from hidden files/folders, and Windows Explorer has a separate setting for them.