I guess my point is, BA sell Flex tickets for 1.5-2x the cost of inflexible ones. As a result of BA's actions, I lost valuable features of my ticket that typically BA charge a significant premium for.

The fact that an agent sold it isn't important IMO, it's a BA fare under the hood, BA plated ticket, BA marketed and operated flights, and ultimately BA who profits from the fare. Using a BA issued upgrade instrument, in line with the instrument rules, and then being rebooked and reticketed (involuntarily) by BA shouldn't degrade the value of the ticket and remove key features.

Ultimately, a negotiated fare is between the TA and BA. The fare rules, issuing restrictions, pricing, fare limitations etc are all items negotiated between both parties, and are all info that BA should have - albeit not in their primary ticketing system, to avoid their sales teams accidentally selling unpublished fares. I get that it's non standard, but someone at BA okay'd AMEX selling this fare.

This feels like a massive error on BA's part. The TA passed literally all the data they had about the ticket to BA, and still BA wouldn't fix the issue.

The way I see it, both BA flight cancellations, and poor internal processes led to me as a customer losing value of a BA issued and fulfilled product.

I guess the net result here is for me to never use IT(X?) fares. It feels too high risk to ever have to deal with this again in future - particularly where I expect to want to make post departure changes.