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Advance document is not shown in Prepayment Recovery option for few reasons, if . If you face such issue please check if:
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2) Order is selected in Payment Document. If an Order is Selected in Advance document, this payment can be applied to the Invoice with this Order only. And, on the contrary, if you have Order only:in Invoice it can settled only by the Payment with the same Order Specified in.
You can specify multiple parameters in Payment document switching to Table Mode:
Functionality described above is applied to Accounts Payable and Accounts receivable sides.