As Andrew has said, since the vacum is released (via N316 valve) by switching the Ignition On, it makes no difference if the vacum has already drained away. If any vacum is still present, switching the Ignition On will immediately vent it via the N316 valve, you may see/hear this venting and the actuator/linkage move. If there's no residual vacum, the N316 will still open, but you'll see/hear nothing (except the N316 click), as there is no vacum to vent, and the flaps have already been opened by the return spring (as the residual vacum drained away)
When the engine runs, vacum is created, the N316 closes, the actuator moves, and the flaps (should) close. I think this fits with what you saw ...
Mac.