The reservation cost is being cleared out when customer cancels booking on Expedia so I cannot charge the cancellation fee.

Answer:

We can't and we don't modify Expedia reservations. Even if we would "blank" the cost in our system, it would merely be symbolic, as it wouldn't be transmitted back to expedia or the customer that booked.  If the reservation cost is no longer viewable, you will need to contact your Expedia account manager to have them research the reason.