and somehow I didn't realize the flight I booked had a 12-hr layover in ATL. We've done this flight many times and it's always a 4 hour layover. It was about a month before I realized what I had done. I spent a while trying to get the flight changed, but these ones were Basic Econ and so it would've cost $99*6 to change the flight. So for $600 I decided we'll just have to suck up the 12-hr layover.

Then a few weeks later I get an email saying our flight had changed. The leg from ATL to SJO that we scheduled had been canceled, and they moved us to the leg that we tried to change to. So in the end, our flight got changed to the one we wanted without having to pay the fee.

Sheer dumb luck. This doesn't help you at all. Sorry.