Some guesses that could effect accuracy after a barrel chop,
1) Harmonics of the whole system has changed. With the shorter barrel the projectile may be exiting when the barrel is at a different point of "whip" each time.
2) Velocity change, could try and regain that with reloading but again that comes back to the harmonics in a way.
3) Less mass, more felt recoil and more noise. Harder for the operator to shoot accurately.
4) Murphy is a bastard and doesn't like it when people tinker with things?
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