The value in removing the course from the list is there is no confusion as to which course is being used. With the course list now being pretty much accessible to anyone who wants to look at it, I can see where such confusion would be possible, especially when there are multiple courses with the same name. We sometimes get around that by including the year in the course name, but not always.
That being said, I'm with Jim in my opinion that we shouldn't remove a legitimate course from the course list, even if it is no longer being used by the entity for which it was originally measured and certified.
I'd think the guidance to send out to measurers and certifiers is that if you put a course number in the "replaces" field on the application (and thus on the certificate), that course WILL be removed from the course list, so if the old course can still be run, that field should be left blank.