I was having the exact same problem with my PW2.
So I tried a bunch of stuff this night. And I think I was getting in the bottom of it.
What was working: putting all the books in epub, deleting all other formats, and then I had 2 options:
1. Download the amazon metadata of the book, convert to mobi then use the ASIN fix to get the ASIN from Amazon.
OR
2. Clear all ids from the epub file, the only thing that worked lefting was the tags, the rest, including the comments had to be clean. Then converting to mobi or azw3.
With this, the covers stayed. If I did anythig different, it the covers would vanish. If I skipped using the epub and deleting the rest before, the covers would vanished even if the book had the correct amazon ASIN or no id at all.
I tried converting a few to azw3 too with this metod and worked.
I tried doing number 1 and change the cover to another one that I liked better in one of the books. As I suspected, the cover blinked and change, but rater then vanishing, it was replaced with the amazon cover.
Then I was going to do more tests, but my internet went down, so I couldn't. ¬¬
Today, when I woke up, the internet was already restablished and I began to do the tests again but, out of the blue, everything started to work. When this problem started weeks ago, I deleted a book that had the cover in the kindle and sent again, just to the cover disappear. So I sent this file again, without doing anything to it, and the cover stayed. I sent then a bunch of books, doing nothing, and so far, none of the covers vanished. I even delete from kindle e resend the book that I had changed the cover to see if the kindle would replace it againg but it didin't.
And apparently you tried now to use a older version of calibre (that I had tried before, not one as old, but one that was worinkg fine before, with no luck) and worked. I'm beggining to think that the problem actualy just resolve itself, just like it just appperaed before. I'm wondering if you try now to use the newest calibre the problem will be gone for you too?
Anyway, in case the problem come back, we can try those steps, because I think the problem was still persisting when I tried them, since if when I did something different the covers were still vanising, unlike now (at least so far).
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