For flaps, as far as I know you do have to shorten the ailerons unless there is room for the flaps already. I do not think ailerons and flaps can overlap.

So what you are doing sounds correct to me. You are right, it might change the flying characteristics a bit. If you want more aileron authority after shortening them, maybe you can enlarge the aileron control throw somewhat?

Just to avoid any confusion - the above is only applicable to flaps. For flaperons , you should not have to change any control surface dimensions at all.


Krister