The problem here is that Star Alliance airlines do not use the same reservation systems.

Usually, when a PNR is set up at one specific system, in this case Amadeus, the one your TA uses, certain parts of this PNR will be copied to the CRS the individual airline uses.

However, if some parts of the PNR are changed in on of the airline's systems, they do most of the time, but not necesseraly at all times, update each other.

So in my opinion, UA either started a new PNR with the single flight, or they added the flight in the booking, and for whatever reason the GDSs did not communicate properly and the flight did not make it back into Amadeus.

I do not think the ongoing flights will be cancelled. However, for future use, most of the time the easiest way to do this is through whoever you booked the ticket with.