Cylinder heads are heat treated to a T-6 temper, which involves heating the castings to over 1000 degrees and then quenching in water. When properly heat treated, heads or other aluminum parts will not have the heat treat affected by a simple overheating event in the vehicle. However, just like any other process at a foundry, sometimes heat treating is not done correctly, and this can lead to the heads being more prone to softening up with an overheating event. Also, welding of course can cause the heads to go soft.
Having said that, I've seen information from some manufacturers claiming that their heads should not be exposed to temperatures over 250F. Either they are being extremely conservative, or the heads are not properly heat treated; 350F should be no problem with a properly heat treated part.