Hmmm ok I didn't realize your point was for them to uncover the multiple dragons thing as they go. I thought you were baking that into the setting and giving it to them as a given as a storytelling device. That'll require further thought.
(although, prophecy is so twisty, "at his birth she...
How big of book nerds are the people you're going to be running this with? Because I would probably just handwave it for the coolness of the story if they aren't going to bring it up at every turn. If they are going to, I'd just set the whole shebang in a mirror world, in which the threads of...