This issue is also killing us. There is a workaround which is to create a copy (More>Copy) of the invoice when then creates a duplicate, and inexplicably creates the correct template. But it is so very dangerous; duplicate invoices, invoices no longer tied to estimates, it breaks the ability to see the audit trail, etc etc.

Our custom template has all of our payment details on it so we have had nightmares with firms using that as an excuse to delay payment, etc etc. We are a software company too, so it all looks very embarrassing from our side.

We've had to spin up a trial of Xero with a view to shifting over if it isn't fixed soon. The account manager at Xero I spoke to said that he had dealt with at least 15 other administrators who had this issue. :mansad: