How can I enable Transaction Pro Importer to let QuickBooks Auto Assign Transaction Numbers

QuickBooks Desktop (Pro, Premier or Enterprise) > Transaction Pro Importer
You can let Transaction Pro Importer know that you want to use the next number in QuickBooks when importing by selecting the options tab on the first screen of Transaction Pro Importer.  Then select the option in the Transaction Reference Number section:  Let QuickBooks Auto-Assign numbers.

Please note Transaction Pro Importer still requires that you map a value to the QuickBooks field, RefNumber, as this is how Transaction Pro Importer will know how to group multiple lines onto the same transaction.

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