The current functionality of the windchill mass replace of a component in bom structures requires that you insert the line number of the component(s) as well. (this is not a real mass replace).
I am suggesting a real mass replace functionalitly in which the line number field is not NOT mandatory. So in theory, when you enter the number to be replace, it will find all instances of that number found in all bom structures that is added to the change activity of the change notice. When the number is replaced, it will swap it out on the same line number(s) and same quantity.