I have done it both ways. But if possible, I prefer to have it warm. Having the engine warm will mix all the dirt and stuff through the oil and have it suspended in the oil. Then when you drain it, the contaminants will come out with the oil. If you drain the oil from a cold engine, the contaminants will have settled to the bottom of the oil pan and all the dirt and stuff may not drain out.
In the end, it is more important to change your oil on a regular basis than worry about hot vs cold or flushing vs not flushing. Little things help, I am sure, but in the long run, changing it will make the most difference.
