I updated my upcoming AA flight to credit my non-AA partner frequent flyer account (e.g. Hawaiian Airlines). And now the AA flight was removed from "My Reservations" on the web on on my phone app. (I can still look it up using my confirmation # but it doesn't show up otherwise. The reservation desk couldn't get it to show up on my account either without typing in my confirmation code.) Is this supposed to happen?

When I booked a flight on another airline (e.g. Alaska) and used my AAdvantage for mileage credit, the AlaskaAir web site and app correctly showed my Alaska flight even though I had my AA frequent flyer number listed.

AA said that using my AA mileage # is the only way to associate my flight in their system - despite the fact that I booked it on AA.com while logged in. And despite the fact that Alaska bookings can handle AA frequent flyer numbers just fine and still have it show up under Alaska's "My Reservations!"