Big success yesterday confirming upgrade (with paper certificate) at check-in in FLR for my MUC-EWR flight. I had a tight connection from FLR-MUC to my MUC-EWR flight, and when the agent went to look she saw that there were 6 upgrades available (however she had issue because in the system they could only be processed as M&M e-upgrades). The agent next to her said I would have to process at the gate in MUC, but I pressed the issue with my tight connection, wanted to see if they could call MUC to get me on the grading list. She called her supervisor in FLR, explained the situation, and she was allowed to clear it for me on the spot, stapled my certificate to the BP and no issue in MUC (in fact, I just scanned my BP in MUC, they never even collected the certificate when I boarded the plane...). Come to find out there were still open seats in C, but so nice to not have to stress about clearing right before boarding.