Today is a big day for Southwest Airlines as they have completely transformed their entire system over to the Amadeus Altéa Passenger Service System (PSS). While this system has been in place for a few years now for their international flights, domestic flights were running on an old school system that had limited functionality. This system will allow Southwest a ton of more flexibility with their routing schedules. For example, different days of the week can offer different schedules, overnight flights are possible, and they can now automate rebookings when needed.
The only issue with the new system is that when you change a flight made with points it makes it no longer refundable. If you are then looking to cancel the modified flight, the system will not allow the faxes/fees paid to go back to the credit card used to purchase. I’ve experienced this many times with international flights and the only way I’ve been able to resolve the issue was to call Southwest customer service (where they were able to refund the amount paid). The reservation agents and the online system were not able to do this. This will now hold true for ALL flights, both domestic and international. I am not sure if calling Customer Service will still resolve the issue, but the main work around is to fully cancel the flight and then rebook (instead of “changing”). This will keep your reservation as fully refundable. 
From what I’ve experienced on playing on the Southwest site today, it seems like the system is working great and there is no issues with trying to make or change reservations. Kudos to Southwest for a successful go-live!
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Since you probably do not want to “change” a reservation, but instead “cancel and rebook”, that evidently means that the $15 EarlyBird fee that would have transferred to a “changed” reservation will now be lost.
@Miles – Yes, if you cancel, you’ll lose the $15 EarlyBird check in fee paid. That is why I recommend not adding it onto your reservation until closer to your flight.
Except if you purchase EarlyBird closer to your flight, you’ll get a worse boarding position. EarlyBird checks-in in the the order it was purchased.
@Allie – Yes, the earlier you purchase EarlyBird the better your number will be.
That is a great question… I ended up changing a flight today and not “canceling and rebooking” primarily because canceling both legs was the only option and the price increase for both legs was significant, so I did the change since I really only needed to change the return flight, and paid a much lesser amount because it was only for the increase on one leg. Does that mean I retain my $15 EarlyBird upgrade both legs?? It doesn’t say in the reservation one way or the other.
@Becky – You can always cancel just one way of a flight, if needed, by calling Southwest. If you changed your flight (and did not cancel) then you retain the EarlyBird check in upgrade.
Has anyone had issues trying to cancel a previously booked flight? I’m able to login just fine to both mine and my wife’s accounts but if I click on the Cancel button it says the following “Oops! Your account is temporarily disabled. Please call 855-234-4654 for support. (SW900001-OY4ifnXmReG-n6vDUfT-ww).” I called but the rep I talked to had no idea what was going on. It seems to be a glitch because I know my account isn’t disabled…I’m already logged in when I see this message.
Did this get resolved. I am having the same issue.