My Feeling is they reflashed the car to stock. That is, the programming in the ECU from Roush is no longer there and you're driving a stock programmed car.
I've been hearing rumors that this is becoming more common, in part because of emissions updates available. Thing is I don't hear that Ford is asking customers if they can reflash the cars. They just do it.
Now I may not be right, I sure hope I'm not, but it's something to call and ask about.
Anything mechanical just doesn't seem to fit.