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Navigate to the Lockbox Batch record.
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Select the ID from one of the Unapplied types.
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Navigate to the Lockbox Invoices tab. You will see that none of the invoices for the payment are matched. This is what causes the unapplied payment status.
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To fix this, click on the Native Transactions tab, and edit the payment that was created. Here, because we were able to identify the customer, we will be able to see all open invoices for that customer. We can now apply it to the remaining invoice (assuming it is the correct one) and save.
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Return to the transaction (by clicking on the Lockbox Transaction number in the custom tab or going back in your browser). Here, you would see that the transaction has changed to Applied.