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There is no impact on "account payables" in case of Vendor Prepayment.
I made a "Vendor Prepayment" entry. GL Impact is- "Bank" gets credit and "Vendor Advance Payment" gets debit. There is no impact on "Account Payable". So this transaction is not visible in "AP Register". Ideally we should see this transaction( Vendor Advance Payment) on "AP Register" report.
Also this transaction should be visible while making the "Pay Single Vendor". In order to apply this payment we get an option on vendor prepayment transaction only. I would suggest that this transaction should be available while making the "Pay Single Vendor" also.
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