It's what Chris described.

If your voucher or mileage upgrade is still waitlisted at T-3d they pre-emptively deduct them from your account so that the upgrade can be processed at any point up to departure by anyone involved including the gate agent.

If the upgrade still doesn't clear you will be refunded in the week following the flight, usually within a couple of days.

So you are still waitlisted, keep those fingers crossed...