My colleague and I are flying SFO-LHR on Thursday and return GVA-SFO the next week on W fare. Itin booked 2 months ago with PMUA. We have applied miles+co-pay for upgrades (SWU's already used up!). Upgrade cleared immediately after booking on the outbound, still waitlisted for the return. I know that we are now supposed to pay the co-pay in advance. Does this apply to itins booked PMUA? Do I need to call (boy, am I hesitant to suffer through that) before T24 and pay? If I call, will the reservation get screwed up so that we lose the upgrade?

Advice is greatly appreciated.