I started to put bungee cords across the rain fly from side to side which limits (does not stop) the flapping. The cords are attached to the buckles that hold the fly to the tent. I found cords that are not to tight, just snug enough to hold slight tension. This is for when the rain fly is down which I will do if I expect wind.
I have also been thinking of making connector straps with the same buckles as the tent, to go from the rain fly to the tent body when the rain fly is up, but I have not gotten around to this one yet.