So, following up on this, I went to the counter, prior to boarding, to upgrade to the 'A' group. Once that was done, I told the lady at the counter about the Early Bird situation. More specifically, if that charge could be refunded or applied to the return flight.
She said, that it should be applied to the return flight automatically. She was able to confirm in the system. Sure enough, I had a low 'A' boarding assignment on the way back.
At the time I paid for it, there was no error message, just a normal confirmation message and the reservation immediately showed an Early Bird applied. I still have the confirmation email.
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In case anyone stumbles onto this thread, I have made this mistake recently and can confirm the issue.
I checked into my flight close to 24hrs before departure and received a C10. Since I would be travelling with 7 year old who is too old for 'Family Boarding' but too young to really sit alone, I needed two seats together. The Southwest app let me buy Early Bird check-ins AFTER I was already checked-in. My card was charged immediately.
It was a mistake on my part, and I thought I would be able to get a new boarding assignment, but no dice. Nothing happened. So now, I'm out $40 for a useless Early Bird, and now I have to pay another $80 at the gate for an A group boarding assignment.
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