I would say most definitely, it will affect your arrow flight. To maximize accuracy, you have to maintain consistency from shot to shot. The drag on the arrows with a replaced helical vane will be different than those with your "normal" vanes.
If you shoot at longer distances, you will be able to tell how much of an affect it is having on your arrow flight. Also, that will probably translate into different points of impact using fixed blade broadheads.
Just from the mental aspect, I always want everything the same, otherwise I would always be wondering if it was the arrow or me.
Yeah I would have appreciated maybe a "Hey, this fletching might make your arrow fly differently..." Nope, just slapped them on there and I guess expected me to not say anything. Of course I asked him about it and he told me how much better the helical fletch is. I would have made a stink but didn't know they would fly differently.
As for the helical fletching flying better, they very well might, but not when all my other arrows are straight fletched!!!
The one he fletched shoots higher than all my other regular fletched arrows.