I feel like I am going thru the stages of a mistake fare with my IRROPs saga today. Was scheduled to fly CLD-LAX-EWR-BWI on an N fare today (OW MR), Reverse is booked on a separate PNR for tomorrow. Departure time for CLD-LAX comes and goes at which point we are told there is a delay, and then about 10 minutes later, it is cancelled. SO I get in line and the nice agent books me out of SNA instead (more convenient for me since I live 15 minutes from SNA) and I figure I'll file for ORC afterwards. She knows I am returning the next day on a separate PNR and it doesn't make sense to come back to CLD since I am driving myself, so she changes that itin to return to SNA as well (again, I figure I'll file for ORC).
As she is modifying the second PNR, I noticeon the mobile app that I am being offered the auto upgrade on the outound (SNA-ORD-BWI), so I snag it and realize that she has rebooked in full Y! I'm overjoyed since none of my CPUs cleared. At this point, all 4 segments are in JN.
After she is done with the second itin, I get the same auto upgrade notification (again, full Y) and take it. Once I get to SNA, I look at the second reservation and see the dreaded red text - "A change has been made...". So I go up to the gate agent to see if she can clear it (I can't check in online because of it). She is able to print out BPs with F seat assignments, but there is no Pre indication (SNA printers are apparently incapable of this). I look online and I still have the red text and I can't get mobile BPs. So I call UA and after a very long time they say they fixed the problem. Apparently I requested the UG before the reticketing was complete which hosed everything.
After I get on the plane in SNA I look at the reservation and can indeed get mobile BPs, but now only the BWI-IAH segment is in JN, the IAH-SNA segment has reverted to N
So I call again. They explain that they have put that segment back to the original booking class but "allowed" me to keep the upgrade on the first segment....implying that I never should have been booked into Y (which is probably true). So I hang up.
Before we take off I notice that I have no sequence number on my mobile BP from IAH to SNA and I am not on the UG list. When I get to ORD, I fix that too but unchecking and rechecking in and now I have a sequence number and am at number 9 on the UG list

That's never going to happen. Probably should have just kept my mouth shut and reprinted at check in at BWI or at a kiosk at IAH.
Now I have no idea how the flights will credit. If the outbound and return were to post as full Y, I wouldn't have claimed ORC since the Y bonus would be better than ORC. However, if the return posted as N, or mixed, I'll probably have to claim ORC on that, which ought to be interesting since it is on a separate PNR from the original flight that went MX.
So to recap, not in F, cancelled, in F all the way, and finally in F part of the way with no shot at a CPU on the missing leg