We have a saying: “If it’s going to look ugly either way, you might as well get it right.” Having said that, there is no provision in the rule book that permits throwing the flag for a live ball foul retroactively, after the ball has subsequently been made ready for play.
By the way, I lived through almost exactly the scenario you described, except it was for the winning score in OT, and it was a “covered” tight end who caught the TD. We swallowed hard, apologized, and lived with it. To this day, there is a Hall of Fame coach who left NWI for Warren Central and then Avon, who reminds me of that play every time I see him. It happened in 1987.