It may be that what they showed you was an internal request for a refund to be issued, and that the refund would actually be issued elsewhere and later.
Even if that's the case, that should be enough to sustain a "missing refund" dispute. There appears to be no disagreement between the cardholder and the merchant that a refund is due, and the cardholder has proof of this from the merchant. The OP should pursue the matter on that basis. To restate what I said earlier, the OP should not mention the original situation, what lead to money being owed back to them, or any of the other details of what is likely to be a drawn-out drama. Many people are tempted to do just that, in order to establish to someone (anyone) just how wronged they've been and how unjust the situation is, but when they do so in this sort of situation, they do so at the cost of making it more difficult to get their money back, as it distracts attention away from what is needed to resolve the situation. Focus on the missing refund that both parties agree is due, and nothing else.