I wonder if it could be because the flexible rates are sometimes still prepaid with Amex Travel, and it's easier to refund than to try to modify a charge.
Also I did want to remind you and others reading this, that it's best to book the new room and then cancel the old one... Since inventory is dynamic, you releasing a room could cause rates to go back up in the interim. This was something told to me so I wanted to pass it along.