could in the long run if you jerk it around enough. it's best to do what vance & hines suggested - or put back OEM harley on it
you cange that you change the air flow
air going one way exits pipe but (are you an engineer ?) sophisticated equations set up and send a vacuum pulse toward the valve to help it close. this matters more on cheap engines and or bikes tuned for highest performance (valves greedily adjusted they even do a thing now which while balancing pressure out and back pulse to pull valve also the pulses cancel to reduce noise (on cars)
wrong back pressure will cause engine to run poor and that in turn can cause in a long period of time: gum up engine and valve problems
so. unless you really want to do the engineering on air flow for your (current mods) for a harley
don't mess with it - not worth it. i hear baffles are good if you can afford them and they are SUPPOSED to be there
if they are supposed to be (designed to be) there
you pay to put them in would anyone do that if they weren't good ?