They should be able reinstate the ticket they accidentally refunded, apply the return flights you actually flew to that, and refund the walkup ticket you booked. I had a situation a few years back where during massive IRROPS in ATL, nearly nonexistent flight options, long wait times on the phone and jammed SCs, I bought a walkup ticket to hold space on a recovery flight. When I finally got through to an agent, they were able to sort it out and refund the walkup ticket. It took the intervention of Global Ticketing (naturally) but they got it done.

A key difference with your case was I hadn't yet flown the flight...I imagine this may make it more complicated or maybe so troublesome it's not worth the effort until you get to the right person. But given the circumstances, they should be able to fix this (even though it's not your money) and then also probably make you whole through some additional customer service gesture.

I wonder if they botched other reservations as well.