A pass upgrade can be made over the phone if for some reason it does not work online.
The one time I did this, because the site was down and they said to, the phone agent put it through as a cert upgrade. My TA and AC both said it should be no problem, it was showing as complimentary, but the gate agent was looking for a cert (I was still basic then). So make sure you get the right kind of upgrade and if your BP prints with "CERT", I'd consider cancelling and rebooking if there's space to do that.
=aw