In CF's I believe it is 100 fps loss for every inch of barrel loss (approx). As for ML's it would have to depend on your charge and what the barrel is capable of burning within that length. I would think that if you were to bump the charge a bit in the shorter barrel you could equal a lesser charge in a longer barrel.
Does any of that make sense???
edit: I never did reply to the question. ...Yes with the same load there will be a "difference" Bump the shorter barrel by 5-10 grains and it aught to equal out.