Yes plugging does affect a bowling ball, you have to think the when you drill a ball you drill in to the core changing the dynaics of it. Plug is only 1 density so when you plug a ball you will again change the dynamics because bowling ball have 3 diferrent densities: core=high density, filler=low density, cover= medium density. Most people wont notice the difference but I don't recomend buying a plugged asymetric ball unless your driller has a Morich Determinator, because once you drill into an asymetric ball the mass bias actually moves from the marked spot on the ball. The determinator can locate the mass bias by spining the ball till it the ball rotates around the Prefered spin axis/mass bias and then mark the true location of it.
Other than that just try and try to make sure the plug is out of your track like the above two said.
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"Viva la Nacion De Brunswick"
