2017 Prius engine swap affects AC system

I recently had an engine swap at a Toyota dealership. The AC did not work immediately after pick up, we called in and let them know we would return the vehicle. When they did the diagnosis they said the serví motor and the air box went out? I responded saying the AC worked fine before the engine swap and they should repair it as they had to have disconnected it. Does anyone know if the engine swap would affect the AC system?