OK, so here is my update. I hope I can deal with this somehow.
When I accepted a bump last month taking SFO-YVR, instead of SFO-SEA-YVR, I got 500 miles of credit on the original Air Canada flight for SEA-YVR, but not for the actual flight I took. So this is about 300 miles. The agent said he was unable to put my Aeroplan number on the boarding pass for SFO-YVR, but at least there is no Mileage Plus number on it. So if I submit this one, I should get the 500 miles removed, and instead get the 800 (or so) miles for SFO-YVR?
For my United flight FRA-SFO two days ago, I had to check in at FRA. The Lufthansa agent (because Lufthansa seems to handle United check-in at FRA) would not reprint the pass with the Aeroplan number on it, although I explained the situation to him. He said something like, "Oh, the Aeroplan number is in the system." The UA Mileage Plus number was on it, but he would not reprint it. So I find that this flight segment has posted to UA Mileage Plus, but I don't know what I can do about it. I'd rather get Mileage Plus than nothing, but I'd prefer Aeroplan. Any ideas?