The CRM Unleashed integration does not import a customer reference from the Invoices endpoint. This causes the field to be "lost" when an order is progressed to invoice.
We could look into a way of requesting this from Unleashed, or if not accessible, perhaps cache the value we have imported, or look up the original order to pull the customer reference from that.
Unfortunately the Unleashed API doesnt provide a customer reference for sales invoices. It only provides this on sales orders, not invoices. Unleashed would have to add this to their API in order for us to add this data in the CRM.