"Punch In" and "Overdub" usually refer to the same thing.
It would be useless if the process required a complete re-performance of the track, overwriting everything that's already been recorded, instead of overwriting only the part being overdubbed between the punch-in/out points.
But if the owner manual is silent on how to do that, I've got nothing to go by.
Perhaps a DR40x owner will have a workaround and be kind enough to join the thread and share.