Hello Muhammad Fahad,
Even if you create a PO from the agreement; you can still find the prepayment line at the time of PO invoicing. This is standard procedure.
But you have to keep in mind that; you will be able to see the prepayment line at the time of PO invoicing only when you have settled that prepayment invoice through vendor payment journal. Otherwise, it will never appear.
Therefore; do the following;
--- Once the prepayment invoice is posted in the purchase order; create a new vendor payment journal and settle this prepayment invoice there.
--- After that; post the vendor payment journal.
--- Now go back to the PO and do the invoicing.
--- Click on Vendor invoice section and select Apply prepayment.
This time you will be able to see the prepayment line in the PO invoice.
Kindly check and provide your feedback.
Best regards,
Sourav Dam
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