I am having the same problem with Quickbooks invoice emails.  I have a template that I modify with customer specific or other timely information for each customer that I send an invoice to.  I generate the invoice email from Quickbooks.  Then edit it while it is open as an Outlook email message until it contains the customer specific information I wanted to add.  Then I click send.  I always to a CC to my company email. 

Both the CC and the copy in the Outlook Send folder are reverted back to unedited template.  I was embarrassingly alerted to it by a customer yesterday.  I spent 10 hours yesterday trying various things to get the invoice email to keep the edits as well as checking the internet to see if anyone else had a solution or workaround.

No workaround or solution found.

A side note, when a Quickbooks invoice email is open, no other Outlook actions can be taken.  That is, I cannot open another email while the QB invoice email is open (e.g., to copy and paste from there to the new email).