Actually just got off the phone with Southwest regarding the exact same thing. Our fares for Aug. went down by $200 total so they told me to go on-line and change the flight and the early check-in would still be intact since that is a different confirmation number. I just finished changing both of our flights and we are now all set with cheaper fares and still have the early check-in. My only other question would be since we have never flown Southwest, is do they offer you upgrades when you check-in on-line before your flight. We did this on our trip last Aug. with Delta and got the upgrade really cheaply.