Had to be the smoke monster. How else did Ben get a message to her? Did future Ben send her back in time? Not likely. Where was she hiding all this time? Where did she go? The reasonable answer is the smoke monster. Doesn't the smoke monster appear after the whispers? And I believe the whispers happened again and she disappeared. And like Despair said, she disappeared in a flash. So ya, Harper = smoke monster.
Makes sense. This could explain why Ben had lunch with Kate on the beach; he was testing to see if Kate would be a better fit for a replacement versus Juliet.

