Originally Posted by
CO Insider
Specifically, customers who have waitlisted for an upgrade in conjunction with a OnePass upgrade reward will be permitted to stand by on the day of departure whenever their waitlist does not clear in advance. Upon check-in, these customers will automatically be added to the upgrade standby list for any flights that were waitlisted. All day-of-departure standby upgrades will be cleared by a Continental airport representative at the gate once the flight has closed for check-in.
Sounds like you'll be ok. But in a separate post, CO Insider stated that if it doesn't clear automatically (but it should), the phone agents won't be able to help you, you will have to take care of it at airport.