The air conditioning continues to work when the auto stop kicks the engine off but on a lower output. If the temperature inside the car is not near the setpoint, the Stop/Start is not activated. In Houston where it is normally hot and humid in the summer, the Auto Stop/Start doesn't activate until the car cools off and then if you are stopped for long it will restart the engine, I assume to boost the A/C back up. It actually works fairly well.
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