hey tony.
i have drilled a few flanges. and it works as long as it's done properly. toyota makes it pretty easy since the shape of the flange determines the perfect concentricity between the drive shaft flange and the t-case flange. the best way to re-drill a flange is to put the "wrong pattern" driveshaft right up to it, then use two vise-grip plyers on opposite sides to hold the flange in place. use a centerpunch and mark your driveline bolt centers. leave the vise grips on and drill one bolt hole. then insert one driveline bolt and tighten it up. you can now remove the vise grips and drill the other three holes, using the driveline flange as a guide.
the oem flanges and even the aftermarket stuff is more than strong enough to support multiple bolt patterns. some of the aftermarket flanges have up to 5 patterns on them and i've never seen one fail.
sharp drill bit, slow speed, lots of oil,......done.
georg