Jim, I sympathize with your view, and about the only answer I see is that they cannot advertise they are using a certified course. That could cost them runners, if someone who has not run the race before bases their decision on which race to run on the course being certified.
This is why there was a strong argument made for the original measurer being able to submit their original measurement paperwork, if they could confirm there were no changes, and the course is being used as originally mapped. That idea didn't stand up to the RRTC board, though. I would still advocate for this particular scenario being accepted, and only have the race pay $25, or something nominal, for the resubmission of paperwork for a new cert.