If it was refunded to the account because the card was closed (within 60 days), they can see that refund. Unless it was refunded for a different reason.
I believe one was waived, not refunded because it was closed, but I don't really remember.
What I would do is try to open more cards, enough to cover your cards that had no AF paid. Make sure to pay the AF on those, even if they dock 50k your still good.
I did apply for another card, but they wouldn't approve a 2nd card. I do plan on paying the AF on that card (with the $100 Statement credit it won't cost me anything). All I can do is either hope I don't get reviewed or apply for business cards.