I have the same problem since yesterday. I have 3200 books at my calibre and at my Fire tablet. And yesterday/today the newest 4 books aren't shown in the reading app at the fire. Only at the internal storage of the fire and with green indication at calibre.
I followed every step of the help, I was at the help center of amazon (with the great idea to de/new-register my kindle (which deleted most of my collections... so never do that, when you're not always connected via internet!!), but nothing helps.
So I only have now the problem, that the last 1000 books aren't at collections, collections are deleted AND I CAN'T TRANSFER the books. Neither in AZW3 nor in epub-format or in Mobi. Also not working via email (then it's only in documents, but not in the reading app.)
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