I spent an hour on the phone with UA yesterday on this. Since I have checked with the operating airlines and also online with LH (you can't access records online with Swiss), and it all seems normal, my remaining question is why UA did it.
After being cutoff once, I reached a supervisor, though I asked for the ticketing desk and never got there. The supervisor went back and saw that when UA asked Swiss for our two seats originally, only one was released to UA, even though two were available (which I knew from research before I booked the trip). So UA had one seat and had to write back to Swiss to get the second so in order to not lose the Swiss seat they had, they split our trip into 2 UA PNRs, put the seat they had in one and pursued and eventually got the second seat into the second PNR.
Bonnie Raitt does a song called "Easy's Getting Harder Every Day". The supervisor, who sounded pretty aware, said this sort of thing has been happening a lot and many customers are demading that their two PNRs be put back under one PNR but UA's system has no way to do that. I guess I could invest another couple of hours on the phone and demand that they cancel the whole trip and rebook it under one PNR but I'm not of a mind to do that for two reasons. First, as mentioned above, I've checked all of this with the operating airlines and everything looks good (and since the trip isn't until next year, I'll be checking again a few times). Second, rebooking could run into availability issues if the seats I have get gobbled up after the cancellation and before the trip gets rebooked. Or there could be other screw-ups that come out of the rebooking process, so I'm going to go with the devil I know.
Clearly, UA is a wounded bird at the moment-While I wasted a lot of time on the phone, UA is paying people to deal with me and all the others cleaning up these apparently widespread array of errors, which earns UA nothing but bad karma with its customers.