I had a similar issue about a year ago. Used a trip credit to pay for a portion of a new reservation and credit card for the rest.

Ended up cancelling that ticket and they issued a new credit for the entire amount. I asked for a refund for the portion that was paid by credit card and was refused several times as that was company policy.

One DOT complaint later they refunded the amount paid by CC and reissued the original trip credit. Didn't take long either...