Thanks for all the replies.
I did not realise that I am only allowed to post 5 times a day, so sorry for the delay in coming back.
To answer some of the comments…..
Ldnn1 I appreciate that AA has dynamic pricing, but I cannot find availably on BA for any AA domestic flight on any day in any cabin. On AA's site, pretty much every flight in most cabins are available. From what I can see seats can range from 4.5K miles to over 100K, but regardless of this, none that I can find show as available to book with Avios on the BA site. Is there a better way to search for domestic AA seats with Avios?
golfmad you are absolutely right and this is the answer that BAEC gave me after complaining. My issue was that I was given the wrong information by the check-in agent and only paid to upgrade on that occasion in order to get the tier points. It was a night flight so F had no real benefit to me as I was just going to sleep anyway.
Geordie405 - I have now managed to get an Avios seat back in F, so at least I can check out the Chelsea Lounge then. I'm just hoping to get one of those magic agents that RichieMcknows spoke about that knows how to upgrade the JFK-LAX as I imagine that would be cheaper and worth it for the double-tier points.
Volar to answer your question, When I tried to book it online, it kept crashing so I had to book it over the phone. I should say that the LAX-SEA-YVR-LAX is on a separate booking so I won't be getting double avios on those.