Due to the nature of the situation*** the difference would probably fall within the range of results netted by repeating the test using one or the other over again, rather than switching between the two. I'd say this would be especially true if the lower energy one was already well within a normal range of applicability.
For example consider a 300 Weatherby magnum used for hunting elk. (Well within normal range of use.) Comparing it to something else with 20% more energy over a series of shots probably won't show you much difference.
*** Game animals aren't ballistic pendulums or uniform test media.
