It looked like the swap started with the bodies staying where they were, and the consciousnesses jumping from one to the other.
So yeah, then she, in his body, with his powers, caused the craziness at the hospital.
Then when it "wore off", the reverse happened, the consciousnesses stayed where they were geographically in the world, and the bodies just magically warped and swapped back around them.
That sounds like a pretty goofy way for the power to work, but that's what it looked like was happening on screen. Obviously all bets are off if the narration is unreliable.