The last rule book I have is 1997.
On page 302 is a sample application for recognition of road race performances.
Page B, Part II asks that it be attested that the race was run on a course as described on a USATF measurement certificate. This certainly implies that certification must exist prior to the race.
Rule 185 deals with long distance events. I see no explicit statement that the course must be certified. However, it has long been the custom that the course must be certified before the race is run, if performances are to be recognized.
Perhaps someone more up to date on the rules can provide better information.