You may face a situation when the same invoice gets paid twice using the different payment methods. For example, if there has been a delay in reconciling accounts in the accounting package, the autopayment (as the invoice was paid through autopayment) didn’t reflect, and the payer paid through manual bank transfer or any other method. The payment duplication generally happens when the manual payment is made shortly after the auto-payment transaction was processed.


Note: If full payment is applied to the invoice in Xero (and Wise-Pay is set to check updated payments), the automatic payment would be canceled. In the case when a partial payment is applied to the invoice, the automatic payment would be rescheduled for the remaining amount. If the payment is applied after the debit has already been taken, but not cleared, you will not be able to apply payment to the invoice and see the “Fix Unapplied Payments” error.


The following diagram describes the steps involved in issuing a refund and correcting accounts:



The following are the steps to refund the overpaid amount in such scenarios:


1.      Process a manual refund of the amount to the payer either through IntegraPay or a bank transfer.

2.      Remove the payment from Xero and sync invoices

3.      Apply a payment for the invoice and sync payments.


Process a refund of the amount to the payer either through IntegraPay or a bank transfer

Use your payment processor account such as IntegraPay to complete this step. Follow these steps to process a refund through the IntegraPay console:

1.      Log in to IntegraPay.

2.      Search the transaction and click Refund to refund an amount for that transaction.

3.      On the Refund Transaction screen, click Partial Refund, and specify the amount to refund.

Note: Ensure that you have deducted the surcharges paid while processing the incorrect invoice.

4.      Enter your email in the Email Receipt To text area and click Refund Transaction to refund the amount.
IntegraPay automatically adjusts the next invoice with the refunded amount.


Remove the payment from Xero and sync invoices

It is a recommended practice to remove payment from the invoice in Xero and reapply to keep the records updated. Removing the payment enables you to record the payment method through which the payment was received, and also to apply a different amount to the invoice. While reconciling accounts, you can clearly see which payment was refunded and which one was received against this invoice. When you sync payments using Wise-Pay, the payment is adjusted to 0 for this invoice in ConnectWise. Follow these steps:

1.      Log in to Xero and search the incorrect invoice for which a refund is required.

2.      Click the Payment link on the invoice to see the Transaction: Payment page.


3.      Select Options > Remove & Redo to remove the payment from the invoice.
This should remove the payment, and you should see the appropriate success message.

4.      Log in to Wise-Sync and sync payments to change the payment of the invoice to 0. If you don’t sync payments, the payment for the invoice will still be unchanged.


Apply a payment for the invoice and sync payments

As you have removed the payment from the invoice, you need to receive the correct payment to settle the account. The received payment would then be synced back to ConnectWise through Wise-Sync. Follow these steps:

1.      In Xero, search and open the invoice and go to the bottom end of the Invoice screen.

2.      In the Receive a payment section, enter the correct amount and the date. Ensure that you have selected the Wise-Pay Clearing Account in the Paid To drop-down.

3.      Click Add Payment to receive a payment for this invoice.

4.      Go to Wise-Sync and sync payments to reflect the payment in ConnectWise.