Customer refund through eBay pulled funds from credit card instead of bank account

We recently sold an item through our eBay store and they sent us a payout for the sale to our bank account. However, when the customer returned the item and we refunded them, eBay charged our company credit card instead of pulled the funds from the original bank. I’ve contacted eBay to see if this can be reversed, but it’s too late unfortunately. At this point, I’m not sure how to handle this in Quickbooks, especially since I now have a transaction hanging out in the bank deposit screen for the refund. I’m assuming I can create a journal entry at least for part of this. The complex part is that we also withheld funds for the shipping costs to the customer.