In the past when I've booked things on AC.com using a promo code, the promo code would be applied to my modified bookings (when I made the changes online) even after the booking deadline had passed (provided the changed booking followed the rules/dates/blackouts required by the promo). The % discount would be applied to the current base fare at the time of the change (could still result in a fare difference, and if the new ticket is less expensive you forfeit the difference).

Of course, this was a few years ago and things may have changed.