I have a multi-city booking via Swiss on LX and LH metal in a few months - XXX-ZRH-EWR and JFK-FRA-YYY. My plans have changed a little and I want to alter the booking to XXX-ZRH-EWR and JRK-FRA-ZZZ (so the only change is FRA-YYY becoming FRA-ZZZ). My fare rules allow for changes, I have to pay the fare difference. I can pull up my new itinerary XXX-ZRH-EWR and JFK-FRA-ZZZ on the Swiss website perfectly fine, it's about a EUR 400 difference in fare from what I paid for the original itinerary.

Calling in twice this morning to rebook, both agents tell me the difference in fare in their systems is EUR 2500, they are unable to see the fare I can see on the Swiss website - crucially, the JFK-FRA leg in A is only showing in their system as available in F. The flight is LH401 on 17-Aug, which on ExpertFlyer shows F5 A5. Neither agent could book the fare I was seeing on the website. I don't want to change the JFK-FRA flight, just the FRA-ZZZ flight...but even if I did, I can book A on the JFK-FRA flight on the Swiss website so the fare is available.

Has anyone else encountered this issue? Why can't the agent book the available fare? What might cause them to only be able to see a higher fare than the Swiss website?