After a refund is issued, the client then owes that amount refunded - meaning the project will show a "Due" balance. This is to support the common case where a bride will pay, but then the in-laws would want the charge on their card instead. You'd refund the bride so the in-laws can then pay the due balance.
If you're issuing a refund on a project and want to avoid a "Due" balance, you'll first want to add a Discount Service, with tax, to the order. (Article). This will let you track common reasons why the refund was given (such as items not delivered) and will show an "Overpaid" amount on your project.
Once the refund has been added and the contract is resigned, head to the "Billing" tab to view how much you need to refund your client.