Hi @Marko Fazekaš ,
Part of the header that is removed and that contains Jira ticket number is: In-Reply-To: <some jira infomation inside>
Based on my research and test, the "In-Reply-To" header would appear when I reply to a message without changing the message subject. But if the subject is manually modified when replying, seems like the reply won't be included in the same thread as the original message, and there are no "In-Reply-To" or "Reference" header:
So could you check if the message subject was modified when replying in your scenario? If this is the case, try keeping the message subject and see if it helps.
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