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It would not hurt performance by any significant amount, although you would be creating a sort of Helmholtz resonator out of the stub from the cutoff part. That will change the way the exhaust sounds, but that's going to change anyway.
You could perhaps do some calculations and tune it to cancel out any drone frequency that's bugging you. Just need to figure the volume of the dead end cylinder you're making and weld a cap on it.
My 2 cents...
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