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Buy nowLet me share some information about how invoices are converted, RodenA.
Normally, links between invoices and received payments in QBO are converted to QuickBooks Desktop. However, invoices that contain charges, credits, billable expenses, or time associated with sub-customers will be separated into one invoice per customer.
To isolate the issue you can try converting your file again using the migration tool. Make sure to use a supported web browser to avoid errors and unexpected behaviors during the conversion. When you're ready, here's how:
Go back to your QBO file and then prepare it for export.
Take note the rounding differences in the two versions can also cause failed export of payments to specific invoices. When this happens, you'll have to correct the amount on the invoice and then apply for the payment.
Lastly, here are some resources that you can read to learn more about the conversion limitations and help set up your company file in QBDT:
Keep me posted with results as I want to ensure that everything is sorted for you. Have a pleasant day ahead.