Jeremy,
I have seen many early lenses with cut flanges to fit on smaller lensboards. It seems to be a fairly normal thing to do. Charlie's suggestion should also work without the violence to your flange, although make sure that you have enough tooth in the wood for your screws. Mounting a 16" portrait lens on a "tiny" Deardorff will really stress the front standard, so you may want to consider a way of supporting the lens; I have watched these big portrait lenses slowly pull (cantilever) themselves out of their lensboards, so perhaps a small clamp on the front of the lens or something of the sort...