LondonElite

chickenmittens, I don't think you understand. There needed to have been upgrade space at the time you were seeking to use points to upgrade (unless the EK system is very different to most others, which I don't believe it is). The fact that there were empty J seats on the flight itself is not relevant, since EK may not have been willing to sell any of those for points (or points upgrades). This upgrade space is a subset of of the business class inventory. There may or may not have been availability, no one but EK will know that now.

I will say that I don't know what agreement Amex and EK have in respect of these transactions, and it may be that I'm wrong and that EK can/will make the required inventory available to Amex points transfers, but I would have found an exchange like the one you have with the initial agent highly suspicious and asked for a supervisor, or at least for her to read back what was being offered. This doesn't help you know, obviously.

I think you will need to bite the bullet and pay the charge (which is an Emirates charge which you authorised), then work with Amex to have it reversed. Others may advise differently, but I would stick to one channel of communication at Amex. This may take some time and involve people with lateral decision-making ability, rather than just policy wonks.