I don't see why the date / routing is relevant? flight is booked from JFK-HND stopover, HND-CTS in J. i'm trying to change to a different HND-CTS flight on the same day also in J. the flight shows up when searching HND-CTS on AS/QF/BA/AA , as well as when i search JFK-HND stopover, HND-CTS, so it's definitely not a married segment issue.

I'm 99% sure it's an issue with the phone agent's system. In the past, I've successfully booked many flights on the website that agents were unable to see (multiple phone calls, so not an one off issue). If they didn't break the change flight tool, i wouldn't even have bothered calling. Again, 99% sure that the old change flight tool would've just worked ...