I had the same exact thing happen to me! I booked a flight on 6/15 using Apple Pay, received my confirmation via email and the reservation shows confirmed on the SW app. The transaction was showing pending on my card and I went in today to pay it off the transaction was gone. I contacted the card issuer and I was told the transaction wasn’t finalized. I contacted SW and was told it was finalized on their side therefore the reservation was confirmed and ticketed. At this point I’m not sure what to do. Were you able to get the issue resolved prior to your trip? What was the outcome?
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