Tom, you have given us too little information for a definitive answer, I think.
Do they want to keep a common Start/Finish? If so, you could calibrate, then move Start/Finish closer to the loop. But, I think this would require a complete re-do, as the map would have to be changed, and it would not match the map for the old cert.
If they don't mind the Finish being .10686 mile from the Start, you could just finish at the 3 mile, if you calibrated, then measured to the 3-mile spot, from the Finish (unless the 3 mile location was already a certified split). This will verify the 3 mile is truly 3 miles from the Start, and allows them to cut the race short from the certified map. In my opinion, I would then do a second ride, from Start to 3-mile/Finish, and issue a new cert, if the measurements were within tolerance.
I think a new cert should be issued, since the map will have to change. You will have to do at least one complete ride, after making the adjustment, to verify tolerance.
My opinion.