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If SplitVLJournal has been activated, the invoice lines will be populated in the module (Compare above, one line for the total invoice to below several lines of the invoice). This will result in lines only be reconciled if their corresponding payment lines up and makes locating discrepancies easier. This method does require more front end work but may result in less work in the long run.
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Refer to Alternative Methods for Handling Discrepancies if required.