Thanks for reaching out to the Community, pmoriarty.

To verify my understanding, have you already set a default email subject line from your Account & Settings?

If not, you can do so by using the Gear icon, going to Account and settings, Sales, then your Messages section. From here, you'll see an option titled Email subject line, where you can put customized text.

After setting up a custom subject line for emails, check to see if the one you set up is still being replaced.

I've also included a detailed resource about customizing invoices which may come in handy moving forward: Customize invoices

I'll be looking forward to your reply. Have a great Thursday!