People upgrading on LH with $'s, points, or miles need to stop freaking out about the itinerary looking "weird" on the UA website / App. And even ignore the "there has been a modification to your itinerary..." warning (meaning ticket is "out of sync.")

UA uses SHARES. LH (and most other *A carriers) use AMADEUS. They are separate, incompatible systems, and often don't "play" well with each other when upgrading.

As long as the LH segments look good on the LH app / website you are good to go.

Recent story: A few months back I booked BOS-FRA on LH non-stop. Booked as UA code share. Called UA to get flight #'s changed to native LH flight #'s so I could upgrade. Done. So all flights on the itinerary were booked as LH, operated as LH, ticketed by UA. But with zero UA operated segments in the itinerary.

THEN...I went to LH.com and did paid upgrades to business class. They were confirmed on the LH side. The UA side freaked out. All segments dropped. I got an email that "your itinerary has been cancelled". Which is technically true because the originally booked premium economy segments were cancelled by LH and replaced with P business class. So UA showed it as "canceled". And it dropped off the "My itineraries" list. Meanwhile over on the LH side, everything was fine. Confirmed upgrades with itinerary looking perfect, all linked to the original UA ticket number. When day of departure came, I checked in online on LH.com as usual. No issues. Both on the outbound and return. Miles and Plus Points posted as usual. The originally booked segments in the UA reservation was canceled, but the electronic ticket was still active as it should have been.

TLDR: Stop looking at the UA website / app itinerary for partner upgrades. It is meaningless. As long as the UA flights look good on UA side, you are good. As long as LH flights look good on LH side you are good. Don't stress. And whatever you do, don't call either UA or LH to "Fix" it, because all it will do is break it and you'll lose your paid upgrades.