Yes, you can always get a refund for a full flex ticket, or rebook it, even after you've checked in. Your third person has to check in at least 1 hour before the flight, but this can be done 22 hours before departure. If you inform at the gate that you are waiting for someone, they might be able to arrange for them to get off the plane first (if it is a SAS flight), and help them to the gate if time is a problem.

You might get some more advice if you could inform which airport you are flying from, where you are flying to, and which company your third person is flying with.