Faez,
When you entered the Pre-Payment, the system created an “Invoice Number” for it - See Supplier Tracker\Links\Invoice\Open. The invoice number created will be a concatenation of the Supplier ID-YYYY-M-Seq#. Based on the document attached, the Invoice number created by the system should be PPS-2020-2-001. You have to apply this invoice to 1004920. This will leave $300 still open on Inv# PPS-2020-2-001. You can either apply it to another open invoice or ask the vendor to issue you a refund.
I am going to submit a ticket today regarding Pre-Payments not automatically applying. I don’t understand why, when you enter a Pre-Payment and reference the PO why the pre-payment doesn’t automatically apply to the Receipt PO. Then, what’s the purpose of the “Less Pre-Payment” line on the Invoice Header?