There is no reason to call the runner out for entering the dugout. He has passed all bases without being tagged or forced and is considered safe unless an appeal makes him out. Field management would allow you to signal safe for clarification once the runner has abandoned his effort to return by heading towards the dugout. Once the runner has entered the dugout, he is permanently removed from the play. He cannot re-enter the field for any purpose. Since he did, you would just exercise some patience for the shenanigans. When the defense tags the runner and looks for a call, you can state “runner has already entered the dugout and is not in play”. If the manager wants to call time and discuss it with you, you call time and tell him the runner is not in play once he enters the dugout and cannot return. If he asks if the run scores, you simply reply yes. If he questions whether or not he missed the plate, you state simply “coach, that is a question you would have to ask on proper appeal”.
