if one of the large leaves is causing some grwoth that will be later relevant in your canopy (depends a lot on how long you vege and what your intentions are), then i'd cut it off. I don't want a limb i care about stretching 4-6" to escape 1 leaf.
now, if it decimates your canopy, don't do it. try to maintain the same amount of leaf coverage up top. don't create a large gap for nothing.