Talked to 2 crews who had this happen this weekend and neither had issues. 40 seconds is a long time. If the teams aren't ready and the ball isn't set until 22 seconds I wouldn't worry about pumping it back up. You aren't affecting them if they aren't ready anyway.
We had 9 TDs in our game and in all instances the offense was set and ready to snap it at about 20 seconds. Some waited until 5-8 but most snapped before 10. 40 seconds is plenty of time.