Already discussed this on the phone, but just in case.

When a portion of a receipt, which had been entered in Expenses, and linked to a customer as a billable expense, is refunded, the new refund receipt should be entered in Expenses with a negative amount, again linked to the customer. That way, a pool of expense receipts are billed to a customer as an invoice/part of an invoice at a later date, the difference is accounted for, and there is no room for error.