When using the mark as paid feature in AutoEntry and publishing to Xero, the setting for how the invoices are published to Xero must be set to 'Awaiting Payment' under the integration to Xero:

The payment will not process through to Xero if Draft or Awaiting Approval is selected.

To access the integration page simply click on Company settings on the company homepage and select the integration tab across the top of the page. 

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