The balance due for each reservation is calculated by subtracting the amount that has been collected from the reservation from the total payout of that reservation. If this amount is greater than $0, the reservation will have a balance due.
When you issue a refund, you decrease the amount that has been collected, thereby increasing the balance due. If you do not intend to recollect the money that was refunded, you will need to decrease the total payout of the reservation to make up for the difference, You can issue an accommodation fare discount or remove an invoice item, if relevant.