I wanted to chime in here, hoping to save a newbie out there (like me) some frustration. We couldn't figure out why, after changing the invoice template, the custom message showed on the preview but not on the actual invoices.

It turns out, we have to add this manually (copy & paste) to all our existing invoices.  Once the invoice is in the system, it doesn't pull new content changes from the template.  Because we invoice our customers weekly and normally duplicate the previous invoice, make the necessary changes, and save the current week's invoice, this would never show up.  New invoices, 'started from scratch', would bring in the new verbiage.

Hope this makes sense and helps someone else!