Improper Batter

[JefferMC]

How would you handle this one? I don't know that it matters, but rule set is NFHS (JV Tournament)

Home team going on defense in top of second inning substitutes "Number 8 for Number 6, the Flex." After retiring the visitors, Slot #4 (DP) comes up, B1 hits double, becoming R1. R1 gets to 3B when B2 (Slot #5) is retired (1-3) for out 1. B3 watches her third strike go by becoming out 2. Slot #7 comes up, but instead of Number 1 (who is in the line up), we get Number 8 (who, as you will remember, subbed in at the top of the inning for the Flex). By the time the defensive team's score keeper gets this to the head coach, two pitches have been thrown, one a passed ball on which R1 scores. The defensive team gets the PU's attention and explains the problem.

What is the correct resolution at this point? Should the PU have acted when the wrong player stepped in the batter's box? What if the defensive team had waited until the end of the at-bat but before another pitch is thrown?

--- Below is what actually happened ---

First of all, the substitution required a 4 minute conference between the head coach and both umpires before the umpire reported the substition to the other team. When the problem was explained to the PU (i.e. the flex doesn't bat, at least not without becoming a substitute for another player who is batting) he stated that the current situation was his fault as he had given the coach the wrong answer. After another 4 minute conference between the umpires and the offensive head coach, they eventually decided that they gave the wrong substitution (they were confused on which player was being subbed for, which was hogwash as it was confirmed at the time that the substitution was for the Flex) and that #8 should have been subbed for #1. They declared the two pitches "no pitches" and returned R1 to 3B, and B4 resumed the batters box at 0-0, and was struck out on 3 pitches, the runner never got another chance to score.