Wanted to add a data point here. I had an NH J sector (HND-JFK) on a flight which was F6 O0, and waitlisted an upgrade about 3 weeks in advance with PlusPoints.
After applying the waitlist, the PNR on ANA's web site showed HND-JFK in J, then JFK-RDU in coach, then HND-JFK in O (waitlisted).
The waitlist cleared at about T-5 days and the flight became F5. After that, the NH PNR showed HND-JFK in J, then a JFK-RDU in coach (unchanged), then HND-JFK in O.
Viewing the PNR in this state, the NH web site showed a popup message "Since you have a duplicate reservation, this reservation can only be viewed. Please contact the travel agency through which the reservation was made to change your reservation and register your information. For ANA-operated flights, Online Check-in service is available from 24 hours before the departure time.(W_S01P04_0023)".
Indeed I could not edit the reso (no way to select seats on any sectors anymore once the upgrade had cleared). Maybe I could have called NH and had them delete the J sector and reorder the segments; I didn't try since hold times are 2+ hr.
At OLCI I was offered to check in for my first sector (xxx-HND) but was not offered to check in for HND-JFK.
I think this may explain the stories upthread where people had to insist at checkin that they really had a confirmed upgrade and get desk agents to issue the right boarding pass, etc.
Unfortunately I have had a bad cold this whole week and am unable to fly the trip
so I don't know what would have happened at checkin but assume things would have worked out fine. Ah well, NH F another day.