Yes, you need to replace it with another flex-pipe section as it helps prevent the header from cracking under torsional stresses. Stainless isn't any more difficult to weld than mild steel, if you have someone who knows what they're doing. It's very likely the person you're dealing with is welding with mild filler which will cause you problems when the weld begins to corrode with a vengeance.
Find a reputable shop with a better collective IQ and put the right part in there. Flex-pipes aren't terribly expensive and it's a common off-the-shelf component.