I just got a similar bug. I have Lurrus in my sideboard, but not as my companion. In game 2 I changed my deck so that Lurrus was eligible to be my companion. I set everything up and submitted, but my deck was unchanged from game one. My untapped.gg overlay was even confused and showed the deck I actually submitted, which was different then the deck I had to play.
I just got a similar bug. I have Lurrus in my sideboard, but not as my companion. In game 2 I changed my deck so that Lurrus was eligible to be my companion. I set everything up and submitted, but my deck was unchanged from game one. My untapped.gg overlay was even confused and showed the deck I actually submitted, which was different then the deck I had to play.