A course is certified, but come race day, or even while the race is underway, it becomes unrunnable as measured (the road collapses/floods, there's an accident/fire/bomb threat on the route, or the runners are misdirected by a course marshall).
The organizers come up w/ an alternate route that approximates the unrunnable distance. After the race a measurer rides the alternate course and finds it is at least the original course distance.
Should we cut the organizer (and just as importantly, the runners) some slack and consider the course certified as of race date? After all, they had a course measured in good faith, and were prevented from following it only by what some would consider an "Act of (Running) God."
I have had this happen. The course was measured as-run, and times adjusted to reflect what they "would" have run if the course had been the correct distance. The extrapolated time was then used as the qualifying time for whatever race the runner was qualifying for.
Certainly no reason to not consider it certified, if measurements of the as-run AND as it was certified are done (can't be done, though, if the road washed away, or is otherwise un-measureable).
Even in the case where the "missed" portion can't be measured, if a calibration is done, and measured from marked mile points (even if they are not certified), I don't believe there will be a meaningful difference in the overall new course measurement (versus riding from point-to-point on the certified course, then using those counts for comparison of the as-run course).
