It doesn't really matter. Coaches know the situation and 98% of the time they probably won't know or care if he played varsity. Any reasonable coach will understand that they're down there to get work and no reasonable coach would send a varsity starter down to win a JV game.
I don't know how the state would even get tipped off about this. Worst case scenario make up an excuse that he is rehabbing and just there to get some ABs/innings.