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Applying Cash receipts to parent child customers

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Our company receives payment from a parent company for invoices belong to the child unit invoices.  Pretty much it has been straaight forward applying.  The parent company now sends the payment EFT and there is a fee being deducted from the invoice payments.  If we apply the cash received(AR Invoices less bank fee) to actual invoices there will be an invoice that has an amount left that is unapplied on the AR.  What is the proper way to apply this cash to the invoices less the fee for the EFT?


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