I have a flight booked for SFO-YVR-YYZ-DXB / DXB-YYZ-YUL-SFO. There have been a number of minor skchg for YYZ-DXB and DXB-YYZ since I booked it.

Got emails today dropping my upgrade from SFO-YVR and cancelling YYZ-YUL. It appears that I've been booked on a YYZ-YUL direct (so SFO-YVR-YYZ-DXB / DXB-YYZ-SFO). The itinerary now shows:
* Flight 1 (new itinerary): SFO-YVR-YYZ-DXB (probably because of a skchg for YYZ-DXB)
* Flight 2 (new itinerary): DXB-YYZ
* Flight 3 (unchanged): YYZ-YUL-SFO
* Flight 4 (new itinerary): YYZ-SFO

If I go through the self accommodation tool, I am basically presented with options for changing Flight 2 (DXB-YYZ). One of the options is DXB-YVR-YYZ (and it appears to book in R keeping my upgrades). That would misconnect with the YYZ-SFO that the system has booked for me. Anyone know what would happen if I confirm that change?

Ideally, I would be able to change to an alternate YYZ-SFO (direct or not) as my goal is to get more SQM not less. An undesirable outcome is for my booking to end up as DXB-YVR-SFO.