This article covers 

How to fix the Xero Sync Error - Invoice # must be unique?

Summary:

This usually occurs when the same invoice number is already used in Xero. This is a setup problem. You have to check from your end if the invoice in Xero is a duplicate or a different one. Either way, the integration cannot sync this invoice, you will have to make the corrections manually. 

Solution:

This means that there is an invoice in Xero with the same invoice number. Chargebee cannot resolve this issue at our end. We do not know if this means that you have created the invoice manually in Xero or if the numbering scheme set up is the same in Chargebee and Xero and this has led to the conflict of 2 different invoices with the same invoice number (one in each system).

Either way, you will have to resolve this on your end. If this invoice is manually created in Xero, Chargebee will mark the invoice as ignored for all future syncs, if the numbering scheme has led to the conflict, you will have to manually add this invoice in Xero(Chargebee will set up the sync to ignore this error), and fix the prefix either in Chargebee and Xero.