Thank you for your reply. I've been doing the workaround you suggested since the issue started - I create a progress invoice against the estimate so I can track what's been invoiced against the estimate, then I create a copy of the invoice so that I can apply our custom template and I send that invoice to the client as a pdf, then I delete the copied invoice.  It's fine for a temporary workaround but is not ideal in the long run since I do a lot of progress billing. 

My accounting firm contacted their dedicated support rep and informed them of the issue (they said they were aware of it). After several weeks of the problem being unresolved, I also contacted customer support through the QBs chat feature but the rep I chatted with said it wasn't a known issue. Hopefully the update that is scheduled next week will resolve the issue.