Hmm. Did UA claim they also could not see the LHR-JFK sector? How did they expect you to get from LHR-JFK? Surely in the PNR, it will show up as a missing segment in the PNR with no "ARNK" sector for own arrangements, so that should tip them off. I suspect something's jiggered with the PNR. If UA say they can see your flight in the PNR then don't worry it's just some kind of bug between them and checkmytrip reading it. If you're a UA MP member, have you checked "My Itinearies" on united.com to see if it is listed? I would not take some res agent's assurance that "it will be OK" If you're all all concerned. If the sector weas there and it's gone, it would seem clear to me that UA has to fix it - and moreso it should be obvious from looking at the PNR that the sector was there (eg: skipping from say sector 4 to sector 6). Call them back and ask for a sup if they're not helping.

good luck.