I'm in a similar predicament. I was naturalized last year so I went to the Nexus office at YVR to have my US passport added. It was handled by the officer at the check-in though; I didn't have to go in and talk to the ones who do the interviews. He made a photocopy of my documents but did not take my Nexus card (perhaps because it doesn't need to be renewed until 2020). When I tried to use it at a Nexus kiosk, there was a message about "document expired". The US passport worked though. When I got home and logged into GOES, I saw that my permanent resident card was still listed as an "Admissibility Document"; it expired last July although I had already turned it in at the naturalization ceremony. Both my Canadian and US passports are listed in the Citizenship information section, with the US one listed as "Citizenship that you will declare when entering the United States".
I have not yet resolved this issue but here's what I've done so far:
- Called the number for "Updating US passport with Canada for Nexus" listed in the Nexus information thread wiki. The person I spoke with (from Canada Border Services) said that that I would have to contact someone on the US side to have the permanent resident info removed from GOES. Fortunately, the automated greeting on that number included a phone number for GOES issues.
- I called the phone number for GOES. After waiting for over 1.5 hours, when they picked up my call, the line went dead!
If you want to try calling them, the number is 855-873-4637. Call early in the day to get into the queue; as the day goes on, you'll just get a fast busy signal. They are only open until 4:30 pm ET.
- After that exercise in frustration, I've decided to try emailing my question at this site: https://help.cbp.gov/app/ask. I had to create an account and I think I have to log back into the account to see the answer. I don't expect to see anything for at least a couple of weeks. I may try calling the GOES number again once I get over how annoyed and frustrated I am from my previous experience.