A Doozy of a Rule Question

[gotblue?]

Before the third strike not caught (e.g., WP with less than 2 strikes, balk, etc.), the BOO can be corrected if the offense wakes up or the defense "appeals" prematurely. Does the completion of the time at bat, and ripening of the BOO appeal (others have said batter becoming BR) provide the distinction as to whether the run would be counted or the advancements nullified?