BA and most European airlines host on Amadeus, AA hosts on SABRE, so the BA app, which is an Amadeus app, isn't great for AA sectors, which it tends to show for BA codeshared flights on AA only, sometimes the immediately connecting flight. You are genuinely best to use the good AA app for AA flights because the ropey interface between these two GDS platforms, with a history going back to the 1980s, ism't reliable. So if AA changes something, you need to be looking at the AA app.

If there are ghost sectors on either BA or AA, these can cleaned up by an experienced contact centre agent. But it's best to leave them in, cleaning provides no benefit (other than to those with OCD) and you don't want to make a mistake in this area.