I did this exact thing last year (one leg confirmed, one leg waitlisted) and then the waitlisted segment confirmed after expiration. All was fine until about 2 weeks before the flights where the system kicked us back to Y for both segments. It took 3 separate phone calls for them to eventually fix it. None of the reps were ever able to say what happened, and one even told me that the waitlisted one should not have cleared because the SWU's were already expired.