I am a TA, and the only way your agent can change your rates to the lower codes is if they actually booked the reservation through WDW travel. There are hundreds of companies that travel agents can book through for Disney, and many of them offer lower prices, especially if it is a package including airfare. There will be no problem adjusting the rates with WDTC, but if is though another supplier the chances are slim that they will allow any adjustments. So it would be wise to remember in the future to ask your TA to book your reservation directly with Disney if there is any chance of codes coming out.