I was going to start my own thread for this, but I got lazy, and now it fits here perfectly.

A month or two ago, I was bored. Getting antsy from lack of an EYW. Also, I hadn't seen my dad in a while.

I booked SFO-YVR-YYZ (red-eye), 4 hours for breakfast, then YYZ-YWG-YYC-YVR-SFO.

Things were going well, but while at breakfast, TripIt informed me that YWG-YYC was delayed, and I was going to misconnect, which would result in missing either the last YYC-YVR or YVR-SFO.

I did plan to meet people for food/drinks in a couple cities, but YWG was not one of them.

So I had the concierge replace YYZ-YWG-YYC with YYZ-YYC.

In the YYC MLL, I ask to get on standby for an earlier YYC-YVR (YYC drinks didn't pan out, but YVR was confirmed, so I wanted more time there). I showed up as #3 on the upgrade list (because it's not actually an upgrade list), for 4 seats, with 5 people listed.

Eventually, that turned into a checkmark. The MLL agents said they couldn't print the boarding pass, but told me I was confirmed in 3F.

Since I had very little carry-on, I had another spiced rum and Coke Zero in the MLL (gotta love YYC for that rum!), and headed to the gate around T-20.

Y was pretty empty, so they were almost done. I walked to the gate, and said I'd cleared standby. I could even see my BP sitting there. Except it had "MISCNX" written on it.

The "junior" agent called the senior one over.

"How did you get out of Winnipeg?"
"I wasn't in Winnipeg."

Somehow, the original routing was still showing up somewhere. I had watched them delete and add segments in the YYZ concierge office, so this surprised me.

Needless to say, they had to go downgrade the non-rev* out of 3F. 3D and I had an interesting chat about the situation after. I wasn't onboard when it happened, but he heard the whole thing.

Now, I didn't care what seat I got, and my seat had only been assigned when they cleared standby, so it wasn't one I selected in advance.

Had I been in your shoes, I might have requested they put me back in MY seat.

So I think they still see your original routing somehow, and assume you won't make the flight, and offload you. I suspect it was done manually. Mine certainly was.

As for avoiding it... that's tough. In your case, I suspect that because you'd already checked in, it left a remnant of the cancelled flight in DCS when res changed your booking, which is what the GA saw before offloading you.

One time I had a similar situation, which resulted in two SFO-YVR segments and a COUPON REQUIRED on the one I wanted to fly. I had to get the airport agents to offload me, then I called res to get it cleaned up, then I checked back in.

So... make sure you're offloaded before getting reservations to touch the PNR, I guess. That's my only advice.

* I'm pretty sure it was a non-rev, because they were listed on both standby and upgrade lists (i.e. for Y and J), though 3D swears she was a revenue passenger. I can't see how a revenue passenger would show up with both a J and Y priority code though.