If you get a card that is known to work, the odds of toasting the ROM is pretty small. You just need to follow the directions properly and make sure you know what card you have. As long as the card you have is made by ATI you really shouldn't have any problem. Most of the issue folks have now is using cards using the 8500 chipset but not actually manufactured by ATI. The other thing to watch out for is to make sure the ROM you use is set to the right speed, on a LE card, you should use the 230/230 one, on the retail the 250/270 one. But you can figure that out pretty easy by the model number, or by sticking it into a PC.
And yeah, my flashed 8500 LE works great in Jag.
Brian