This article explains how the invoice notes field can be used to populate the reference field in Xero
Please note: At this time this feature needs to be turned on by Cloud Depot for you
Autotask allows you to include invoice notes on your invoices, and our synchronization feature also enables these notes to be applied to your reference field.
When will the invoice note be applied?
If the option to use the PO number as the reference field in Xero is enabled, it will take precedence. However, if the PO number field is empty, the invoice note will be utilized instead.