That is a dilemma! On one hand, if we know a race was not run according to the certification map, we should (somehow) let the runners know. That in itself is difficult, because, unless you are the timer and have everyone's email, there is no way to contact them.
On the other hand, because you are the timer, and you know the course was short, you owe it to the runners to let them know their times are not for a certified distance.
On the one foot, though, you do owe it to your client to not make waves, even when you know they didn't set out the course properly. Or do you?
You may let your client know that, since they (presumably) advertised they were using a certified course, since they didn't use the course as it was certified, you have an obligation to the runners to let them know the course was short, as it was run.
You have your integrity as a timer to consider, also. If runners found that you knowingly gave them results for a stated distance, but it was really short, how does that impact you down the road?
Easy for me to say from afar, but I think you should let the race director know that you should tell the runners that the course was approx. 50 meters short, so they can adjust their times accordingly. Most won't care, but some will.
Good luck!