Well, I suppose it depends upon what type of flaps they are, plain, slotted, fowler, etc.
I've also thought about doing this type of thing. What I had come up with for plain flaps was to separate the flaps and build up some structure on either end of the flap inside the wing. I would then find some brass tubing and/or rod and construct a simple hinge system.
On either end of the flap itself, I'd attach a piece of rod. Then I'd slide some tubing (which should be a snug fit) over both pieces and glue the tubing to the built-up structure inside of the wing with CA. The rod should remain free to move inside the tubing.
I remember coming up with a couple other ways of doing this type of thing, but it was so long ago that I can't really recall what they were! This method must have been the front runner, 'cuz it's the only one that sticks in my mind.
I'd also be interested in hearing others' suggestions on how to make an active hinge for flaps or other control surfaces.
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