if the flaw is in the middle of the shaft it will likely cause the ends to pitch out .003 on a .001 shaft could cause you to have a shaft graded as a .006, bend an aluminum arrow in the middle a little bit and the closer to the ends you get the further they are from straight, when you shorten both ends you moving a bit of sway from both ends, if you cut only one end the center out on one end maybe .001 but the other side could still be .006
however few shooters are capable of the accuracy to tell the difference