I have seen this happen multiple times. Let's say we have a certified Half Marathon closed Loop. The race director would like to run this loop twice, hence we have a certified Marathon. The course search engine would only show the half as being certified. Hence, if the runners want to use this closed loop run twice as a Boston time for that race. Boston, more than likely would reject this.
I don't understand Boston, but is there a solution. I really don't think we should issue multiple certificates.