If they were piping at the surface by the time you got to the pond, then I would contact the hatchery and see what they say. 2000 fish in 3 bags in one cooler seems crowded to me, even if the fish were small. I can see the potential for trouble, such as the failure you describe.
I do think it unlikely you lost ALL of your fish, but there's little doubt that they were heavily stressed by the misadventure.
