It seems that the new fare system took effect yesterday. In addition to changes to the availability of full refunds per fare type, a lot of routes got cheaper. I just got $32 back for an upcoming trip to Buffalo and back on the Lake Shore Limited by going to Modify Trip and reselecting the trains I had already booked, which moved my trip to the new fare system at the lower available price. If you have an upcoming trip, definitely double-check if you can get some money back as well.