How does tracking and duplication work in the event that someone (either inadvertently or on purpose) strips the content of the notification email (rendering it blank) and then replies anyway?

Our notification emails are sent from a special unique email address which includes an authentication code. Anything that users will email to that address will end up in that same conversation. Additionally, we have some heuristics in place that usually manage to remove the signature and quoted-reply text from the message, before it gets posted inside the chat.