Counter to most opinions presented, I actually let the club itself determine what I list on my "courses played" spreadsheet. If the club prefers to designate each 9 separately, then I count them as such [Keith Hills in NC (Orange/Black/White), Blue Fox Run in CT (Blue, Red, White), etc.]. If they promote an 18 and a 9, then I also count them separately [Racebrook in CT].
I reconcile this method by maintain a running column of "total unique holes played" based on the number of holes I have played at each course. That way, I look forward to both "course milestones" [100th course played, 150th course played, etc.] as well as "unique hole" milestones [2000th unique hole played, 2500th unique hole played, etc.].
-Adam