In the end, it was the supervisor who took care of it. The original check-in agent told me “the number was visible in her system”, but the boarding passes she gave me didn’t show anything. That made me super skeptical. So I gave it 5min, ate my boxed breakfast, and went back to the counter with the supervisor/team lead (distinct vest). Honestly, I believe carrying the physical Eurobonus status card (new version with elite plus logo on it) also helped. At least it allowed me to sneak into the SkyPriority boarding lane with approval from the gate agent, and get into the AM lounge at MEX.