I think I figured it out. I created a sales receipt from Square to notate the refund of the $2.75 credit card fee. I created a new item for the refund of the fee and attached it to an expense account with the other credit card fees, versus attaching it to an income account. Quickbooks asked me to confirm that I wanted to use an expense account. I said yes and was able to attached the sales receipt along with the refund to the customer to the same deposit and recorded it with no problem to match the charge from Square.
