You may encounter a scenario where the invoice is showing as Paid via Pencil but not in Xero.
One possible reason for this issue is that the amount due on the invoice may differ from the payment collected through Pencil. For instance, Pencil may have processed a payment that exceeds the current amount due on the invoice.
This discrepancy can occur due to various changes made to the invoice, such as price adjustments, the application of a credit note, or partial refunds resulting from limited stock availability.
In such cases, Pencil is constrained by Xero's rules regarding how payments can be applied to invoices. To address this, we have developed a feature within the integration between Pencil and Xero that allows you to push a credit note to Xero for the affected customer. This enables you to apply the credit note to the outstanding amount on your invoice, while any remaining balance can be allocated to another invoice or a new one.
To ensure that this feature is properly configured, log into your Pencil account and navigate to Integrations -> Xero. Confirm that the “Enable pushing payments as customer credits” setting in your Xero configuration is toggled ON. If it is set to OFF, switch it ON and remember to save your settings at the bottom of the page.
Once the settings are confirmed, you can return to the Invoice page in Pencil and re-push the payment by following the steps outlined in this article: How do I re-push a payment from Pencil to my accounting software.