When a customer has made a pre-payment on a Sales Order but no invoice exists in NetSuite to match to. The Bank Reconciliation tool will allow the user to match the transaction to a Sales Order before it is converted into an invoice, the pre-payment will be automatically be already applied to the invoice.
Step-by-step guide
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7. To find the deposit back, go into the Sales Oder and you can find the deposit under "Related Records" tab. 
8. At the time when the Sales order is made converted into the an invoice, the payment is automatically applied to the invoice and the amount owing is reduced by the deposit(ed) amount(s).
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