Unreported Substitute
 

Bases loaded, batter hits one down the line that clears the bases. LF throws BR out at 3B. OC then informs you that LF is a substitute that was not reported. You confirm it, enter the new LF in the proper place in the lineup, and issue a warning. OC wants the BR declared safe @ 3B. Your reply?

What rule set because it is going to make a difference?

Fed & USA

For NFHS you had the correct ruling and you just tell the coach all action stands.

For USA, and assuming it is a legal substitute, the offensive coach gets to take the result of the play or return all runners to their bases at the time of the pitch, return the batter to the batters box and assume the original count. The unreported sub is officially entered into the game. And, USA has no warning to the coach.