With normal email notifications, the subject of the email includes the issue id in square brackets (ie, [ABC-132]). I've noticed that email notifications from Jira Service Desk don't include this, but instead have the name of the service desk in square brackets. Yet when the user replies to the email, the Jira email handler is still able to add the reply as a comment to the correct ticket.
I'd like to better understand what it's doing to map the email reply to the correct ticket so I can have confidence in how it works.
JIRA's email handlers use a number of different things to correlate email back to issues. Standard email headers are the first line of defense—it uses the In-Reply-To and References headers defined in RFC2822. If those aren't present or don't map to an issue then it looks in the subject for an issue key.
Hope this helps,
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