Hi Nick
The defect (or cosmetic as it is called in ISIS) map is to catch the hot and warm pixels which will have unreliable values after the dark subtraction (ie the pixels will either already be saturated or will become prematurely saturated during the exposure, so the dark subtraction will not work correctly.) The same procedure is sometimes used in imaging where it prevents dark holes appearing in the image after dark subtraction where fully saturated hot pixels are for example. The cosmetic file is generated from the master dark and a threshold is set above which the pixels are considered defective. I have mine set to 500 currently which is well above the noise and generates around 100 pixels in a 10 min exposure with my ATK314
Cheers
Robin