No, all messages cannot be recovered by Facebook. Read the article - messages that are not yet delivered can potentially be read; if it has been delivered it cannot be retrieved.
Unless the key-change forces the user to be using an insecure key-pair, but is that actually happening?
It is hard to check what WhatsApp does, but in Signal it is not the server, but a recipient who sends delivery receipt. WhatsApp then has to either recognize encrypted receipts or allow only one-way conversation during attack. Carrying out the whole attack just to decrypt "hi, are you here?" is not really interesting.