What I meant was that my reservation in UA is telling me that my PNR for Brussels is now the same as the one for Lufthansa although it gave me the actual PNR for Brussels before.

On day of booking this is what it said:

Other Airlines booking codes:
Brussels Airlines: ABCDE
Germanwings: POIUY
Lufthansa: POIUY

Now, it says:
Brussels Airlines: POIUY
Germanwings: POIUY
Lufthansa: POIUY

Where ABCDE still works on the Brussels site and POIUY does not. Using ABCDE on Brussels correctly shows the leg before and the leg after the Brussels flights. Using POIUY brings up nothing on Brussels.

So, nothing has actually changed. The UA website just started lying to me about what the PNR is for the Brussels legs.