AP Standard Invoice Amount Wrong at the time of full payment.

Dear Experts,

When we entered a prepayment for the vendor and then we created a standard invoice for the sane vendor. We applied the invoice on prepayment but after company decision prepayment is unapplied but when we are going to create pay in full then invoice amount in still short which is exactly prepayment amount.

Please guide what happen even prepayment is unapplied.

Regards