Managing Cancelled Flights in OpenAir

We are having an issue tracking cancelled flights and I was wondering if there are other people who have the same problem and what they are doing to manage it. 

Flight is booked
Employee creates and submits expense report for flight
Employee is reimbursed for flight
Flight is cancelled
Employee now has a flight credit

We need to devise a method to reverse the full flight amount less the change fee to the Customer A and efficiently bill Customer B who the flight credit will be applied towards without accidently reimbursing the employee twice.  Employees are creating non-reimbursable receipts for billing Customer B for the flight credit that they have already been reimbursed for.  But sometimes the flight is more than the credit which requires two different receipts - one for non-reimbursable and one for reimbursable.  Then this creates questions from the customer when they see this detail on the invoice as to why there