I know this has been hard for you, @mdmason. I can see the inconvenience of putting so much effort into customizing an invoice email template and not being able to utilize it. Your feeling is valid and I truly understand your sentiments. No worries, I'm here to make this up to you by making sure we're able to properly customize an invoice template so it will show on emails.

To start with, I want to make sure that we're on the same page in creating a customized template. I'll be including the steps and some screenshots for your reference:

1. Go to the Gear icon then select Custom form styles.
2. Hit on the New style dropdown then select Invoice.
3. When you click on the Content section and select Footer, the message you'll going to put in that area will reflect on the official invoice form.
   
   
    
4. When you move on to the Emails section, the Message to the customer portion will be displayed on the email received by your customer prior to viewing the actual invoice form.
   
   
   
    
5. When finished,  hit Done.

Now when creating an invoice, be sure to use the created template by clicking on Customize.

However, if the customized email template doesn't carry over when sending it through email, I'd suggest using an incognito mode to see if it's a browser-related issue since the browser stores cached files every time we visit a site which causes the system to behave abnormally. If this works, you can clear your browser's cache and cookies, or use another supported browser if the issue persists.

Lastly, I've included this article that you can use in properly recording invoice payments to balance your account: Record invoice payments in QuickBooks Online.

I'm still all ears if you need further assistance with your invoices in QuickBooks Online. Just add your reply below and I'll circle back to help you. Keep safe.