I'm not sure I would believe the explanations you have been given – not because they are wrong, but because generally agents don't have any basis for explaining why something is not possible ... the computer says no and that is it.
That said, NRT-PVG must be a codeshare on JAL or a JAL-marketed flight and that may well make upfaring more complex. You don't say what fare / cabin that is booked in.
I think the simplest way forward would be to find a price for what you want to upfare to on aa.com and call and ask about that option explicitly. If the flights you want cannot be found / booked on aa.com then an agent probably can't do it either. It does seem to me that if you can construct a new ticket for the flights / cabins you want then they should be able to upfare it, but that doesn't mean you can find the agent who can do it
