I am having the same problem as well, and was told the same thing that it was an Outlook issue, not a QuickBooks issue.  I just updated to the latest version of Outlook 16.0.13801.20266 and still have the problem.  

I did find one work around:

1. In Outlook, and from the Send/Receive ribbon, click "Work Offline"
2. In Quickbooks,  create and send your message as you have. 
3. In Outlook, open the Outbox, then open your message.  (It will have reverted back to the original template at this point.)
4. Make your change(s) again in the message, and close it.
5. Reopen the message in the Outbox.  If it worked, you will see your changes.  You might have to repeat these two steps until it works.
6. When the text is correct, click the SEND button in your message.
7. Go to the Send/Receive ribbon and click Work Offline to put it back online.
8. The message should be sent - you can click "Send All" to speed it up.  If the message is not sent, open it and click the SEND button again.  You will see that the name of the person is in italics when you know it will go out.

Convoluted?  Yes, but it does work!

To me, this is a QuickBooks issue:  there has to be some communication between Outlook and Quickbooks since you can go to the Sent Email tab for a customer and see when an email was last sent.  I have two different paragraphs that I use from my template depending on the type on invoice-and occasionally I go completely off script and I use my own words. But I at least know when the email was sent.   This is an important tool for us and I would like to see this issue resolved.