I am pretty sure i got this right but need confirmation.

Wholesale subs made. Girls mess up the batting order. 1st pitch of the inning. Defensive team informs me of girl BOO. We get the right girl in the box, assuming the count. Defensive team swears it is an out. I say that is ASA. She says defensive team catches the BOO it an out. I stuck to my guns and I believe I got it right.

Thoughts ,rules references, comments appreciated.

NFHS 7-2-1 "A batter shall be called out on appeal when she fails to bat in her proper turn and another batter completes a time at bat in her place." In your situation she had not completed her turn at bat so you were correct in putting the correct batter in the box assuming the count. The team that appealed needs to brush up on their rule knowledge and should have waited until her turn at bat was over. It would also not be an out in ASA. The same rule application would be used.

In every code I know of, the improper batter can be replaced without penalty until the at bat is completed, regardless of who discovers the error. The proper batter then assumes the count. Nobody could be confusing one code with another. The other guy simply doesn't know the game.

It's not ASA, either. Your call was correct in both NFHS and ASA.

For the out due to BOO, the improper batter must complete her turn at bat and the appeal must be made before a pitch is thrown to the next batter.

ASA and NFHS differ in which other outs stand on the completed play, but your situation never got that far.

Blind Squirrel
 

Well I got the Fed part right because I knew. Now I know it for the ASA world. I assumed because the one coach is a legend he knew ALL the rules. My bad.