If the arrow stiffness and other dynamics are the same, yes. There will be a trajectory difference. The heavier arrow will not drop speed as fast thus reducing the time of flight and subsequent trajectory differences will result. Now it isnt really that simple. If you have a heavy fatter arrow that doesnt recover from the shot as fast as a skinny arrow that recovers faster yet is lighter, they may be a wash.
There is more to arrow ballistics than strictly weight and speed.
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