I resorted to landing from ITA into AA using Powertools this week for just this scenario (BA flight numbers on AA metal throughout). BA wouldn’t land at all - I don’t think it likes MCMC. You have to use the European AA sites as the US/UK link interprets any economy as basic fares AFAICT, giving you the option to change which then puts all legs in main cabin.

AA then made a right horlicks of cancelling one and ticketing the other - going so far as to claim repeatedly it wasn’t an AA booking (said it was BA) despite having both myself and BA on the line telling them it was an AA.com Germany booking! Finally managed to escalate sufficiently to someone who, while never acknowledging that they’d been wrong, managed to sort things out. I need to write in to BA to commend the agent and manager who stayed on the line through what turned into a two and a bit hour call.

Moral of of the story: make sure you chase until you get a ticket - I’m pretty sure had I not done so I’d have found my booking cancelled after a few days. As it turns out, calling BA would have been rather less stress!