I've had this happen. Flying EWR-FRA-ZRH, with the second leg on LH metal, and I could only get the boarding pass for the United leg on the app. The LH app couldn't produce the boarding pass either. Then at the UA EWR checkin counter they somehow couldn't make it happen. Called GS, couldn't help. The agent at the Polaris lounge couldn't either. They all expressed confusion but also seemed sure that I'd be able to easily get the FRA-ZRH BP in FRA. I thought about heading to Terminal B to try the LH counter but decided not to go back and forth through security again. I just somewhat nervously decided to see if the agents were right.

It turned out it was super easy to get my LH BP in FRA. Right when I got to the concourse for the FRA-ZRH leg, there was a LH service desk whose primary purpose seemed to be to hand out BPs to pax like me. There were a dozen or so people in line ahead of me but they were moving fast. It was probably a three minute experience.

I would hope it's a similar experience in MUC.