You are correct, a short barrels is not less accurate. ShortENING however is a different matter, things can go wrong in that process.
My first thought would be that it might just do better with a different ammo, but you thought of that one already.
You have obviously had your rifle apart before and know how to put it together therefore, so not the answer.
Given that the muzzle end of the barrel is where it was worked on, have you had a magnified look at the crown? A good mobile phone camera on macro will often help, stuff a bit of toilet paper inside the barrel, 2-3mm back from the crown, for a better view (too far back and the camera focuses on the paper!).
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