Just to close the loop on this, here is what happened.

First a bit of background. My initial flight was direct YYZ-GVA with a stop in YUL (ie one flight number). I decided to stand by for an earlier YYZ-YUL flight so I could enjoy the international lounge at YUL instead of the domestic lounge at YYZ. I also asked the agent to put my AE number on the ticket instead of UA number. That was fine except when I got to YUL, I asked agent to verify that AE number was on 2nd segment. That’s when I found out I had been offloaded from YUL-GVA! Guess I shouldn’t have messed with the ticket as it took another 20 mins to get me back on the flight.

Neither flight posted automatically to my AE account. After 8 days, I submitted a missing flights request. The YYZ-YUL flight was denied, but the YUL-GVA flight was accepted and has posted to my account.

I have no no idea if my messing with the ticket caused me to lose the YYZ-YUL segment or got me the credit for YUL-GVA. YMMV