Yes paper tuning is mostly for up close, , BUT it will show if the arrows are twisting and cutting in all different ways, as if flying bad, and not just you aiming off target
like if one arrow is kicking up and another down, and next to the side, that to me shows more of a flying issue, and not just havinga harder time holding a aiming spot group!
you say your bow is in tune and paper tested, but when was the last time you checked?
Only saying things can move and as distance gets farther, small things make bigger problems farther out then!
a string can stretch, a rest or a nocking point can move a just enough to cause a headache

Agian just tossing out idea's to check before making the new arrows up!, as if its a bow/sight issue, odds are it won't do much to cirrect and be starting all over!
Good luck and let us know how it works out!