Martin Tomlinson

I believe the original answer is confusing/wrong - each email will have a unique 'Message-ID' the key to any reply emails being linked to an existing ticket is that the new email will have an 'In-Reply-To' id that is the same as the 'Message-ID' of an email in an existing ticket. 

So this

"When a new email is received, Zendesk scans the message-ID on the email. If that message-ID matches an existing ticket then the email is added as a comment on the existing ticket."

would be more accurate if it said 

"When a new email is received, Zendesk scans for any 'In-Reply-To' id on the email. If the 'In-Reply-To' id matches an existing tickets Message-ID  then the email is added as a comment on the existing ticket."