You can populate the reference field in Xero if you enter something in the Description field on the invoice in Microsoft Dynamics 365. Our connector will pick up the first 255 characters (this is a Xero limitation) from the Description on the invoice and will push that into Xero as Reference.
We have implemented the Reference this way because by default Microsoft Dynamics 365 invoices do not have a Reference field. Many clients create their custom fields for reference in Microsoft Dynamics 365. To avoid mapping different custom fields for each connector/client we suggest that you create code to populate the Description with up to the first 255 characters on the Dynamics 365 invoice and in this way our standard connector will work.
If you wish to switch off this behaviour you can do that under Connectorly Settings.