I went to my TA office and my agent was not in
Give your agent a chance to work on the refund. He or she may not know about it yet. Do you know when they'll return to the office?
I hope your agent *has* dealt with lowering fares and won't give you the song and dance you encountered from the person mentioned in your post. If the lowered price happens before you have paid the final balance it is usual for your final balance to be decreased. At least that is my experience.
Let us know what happens.