Just know that this completely makes it impossible to use estimates as designed.

I found another work around that may work better for some people.  It does have its own issues though.

Basically just create a copy of the invoice, change the invoice number on that new invoice to be the same as the old one.  Acknowledge that the invoice number is the same as the previous one.

Print using the custom template (which will now work again since it's unlinked from the estimate.

Obviously this causes issues when the next new invoice is created since the next invoice # counter is reset to whatever # has been copied.