There is nothing wrong with that manifold which a file won’t sort. Welding it will generate an awful lot of heat which is risking warping it
what is the point. I think you are worrying about nothing. Even if I am wrong what is the worst that can happen
just have to change it again plus some remedial work to sort the problem. If you warp it by welding it then you might have to get another manifold. No choice really.