Let's make sure your employee will be able to change the message for invoicing, Slarty.

For now, you'll have to manually change the email message when sending invoices to your customers. As what @Intuit Zac mentioned, you can click on the Save as draft option on the message section to successfully change them. You can use a private browser to make sure it doesn't revert back to the original message. 

However, if the same thing happens,  I recommend reaching out to our support team so they can investigate further. They have the tools to pull up your account in a secure environment and check what causing the issue. 

Furthermore, learn how QuickBooks categorise your transactions on the correct line of your Schedule C. To give you more information. read this article for your guide: Categorise Transactions In QuickBooks Self-Employed. 

Reach out to us if you have any concerns about invoices or email messages in QuickBooks. We'll always be right here to help.