if u flattened out the pipe but don't have a leak than ur not loosing any performance. The inside diamater hasn't changed any and the outside doesn't matter as long as its still holding up. Now if u rubbed a hole into the header than I see ur concern. If its just flat than don't bother changing it.

EDIT: is it deformed in any way?? When u said flat I understood as the metal is rubbed down but not dented. If its dented than naturally its bad.