My memory of it is somewhat hazy, but until a couple years ago, if you changed a flight and then ended up canceling it then you couldn't get the one-way $5.60 taxes/fees refunded to your original method of payment. Rather, it was stuck as travel funds. Can anyone back me up on this? I think SW made some switch so that doesn't happen anymore...but I can't swear on that because I don't think I've done that particular sequence (or at least I haven't kept good enough track of it that way) since I'm mostly dealing with points. Points tickets cancelations always get the $5.60 refund to the original method of payment. Canceled cash fares now get travel funds with no expiry.
If you change a points ticket because it dropped in price, you get an instant refund of the points, and your confirmation code stays the same. Your change confirmation will also show that you paid $0 fees. This is actually a bit of concern for me since I'll use CSP for the taxes/fees on the original booking. So I can provide documentation that it was used with the original fare, and I can prove the confirmation code stayed the same...but if the flight# or times are different then I don't know if that's good enough if I need to file a claim. It's logical and reasonable to me, but I don't know if an insurance claims person would see it the same way. So I'll probably go with the tried and true straight up cancelation from now on. I do suspect, inferring from something a SW rep told me once, that the boarding number can get worse the closer in to the departure date you've made the booking. I've done many check-ins 24hr prior on the dot, and end up with mid B boarding numbers. The one time I paid for EBCI and got a mid B boarding number, I asked about why it was so far back and was told that one of the factors that went into the boarding number is when you paid for the fare and when you paid for EBCI - the farther out in advance you do that, the better the boarding number. I'm always checking back on SW fares and capturing price drops when I can, so I almost never book just once many months out and leave it be.