They aren't traumatized, they're terrified. Without cover, they just know anyone coming to the surface or breaking formation is going to be eaten by a passing heron (or hawk or cat or snake...). Give them something so they can't see the sky - an umbrella, a pond lily...
You can't replace that much water and add a filter on top of it without losing fish - there just isn't enough bacteria left to do the job and there was also a major water chemistry change they had to deal with. I'm surprised you didn't lose all of them.