This happened to me just yesterday, I rebooked my sister's flight for her at the lower fare. Originally the cheapest flight available on the day she and my nephew have to fly home cost her $146 one way each for the two of them. Yesterday I checked and her exact flight was available for $54. I changed it and she has $184 credit, which she should be able to have refunded to her credit card since the only thing that changed was the flight's price (i.e. she didn't take a different flight to get a different price) I've been able to do this in the past too.
Here's the thing...immediately after rebooking for her, I checked, and sure enough the flight at the cheaper fare was gone. This has happened to me before, and on a phone call to customer service I asked a SW agent about it. She said there are only so many fares on a flight at the lowest rate. Another passenger probably cancelled their low fare, so it becomes available again until someone snags it. So 2 seats were available for the lowest fare on my sister's flight, once I booked them for her, they were gone.
So yes, it pays to keep checking...