Expense - Travel Auth (Ways not to encumber certain line items)

Very unique business case situation - In few cases the departments pay for travel and then employee is not -reimbursed. So when employee create the expense report, will only reimburse the other line items that is not payed by the department (for e.g the airfare) from the travel auth, leaving the encumbrance on travel- auth for the non-reimbursable line items.

How do we tackle this situation?

-Sabeer