Having similar issue with my wife. I manage our UA accounts. I also let the computers generate her FF # when the merge happened.
When the system converted from pmUA to COdbaUA, her information was (surprisingly!) in my account as a listed traveler that I book for, and even had her new Mileage Plus number (again, surprising!).
But when I go in to add her passport details it tells me that the name on the account doesn't match her Mileage Plus number -- even though their system is what generated the new info. So I can view her details, but if I hit save even without changing anything it errors out and tells me name and FF # don't match... But if I cancel out, it maintains the name plus FF # just fine.
Near as I can tell, for some reason, sometimes she shows up as first name+middle initial as her first name, other times just as first name, depending on the UA system and position of the moon.
I was able to enter her passport and trusted traveler info on our reservation, but I can't get the passport to save in the travel companions section.