FACT or MYTH? Battery-A/C situation...?

The two worst things for the 12 v electronics in your vehicle are heat and voltage spikes. Your sensitive electronics cannot handle either very often, or for very long. When you remove the battery from a running charging system, you create massive voltage spikes. Your alternator is running hard, trying to replace the current used to start the vehicle, and also producing current to run any operating equipment(heater fan, a/c syst/eng ignition/ etc) By removing the battery from the system, you create a voltage spike when you disconnect, and when you reconnect. Any system that is live when this occurs is subject to the EMP. It does not sound like the a/c system was affected, as the controller is commanding the compressor to cycle, and the hoses are circulating freon. Your fan may not be running(thus the no cold air). Start by checking all of the fuses, for all of the syst. If you find some syst. will not come back on line, you will have to get them checked, professionally.