It appears that when a message is transmitted through the Microsoft Outlook SMTP server <smtp-mail.outlook.com> (or perhaps any Microsoft SMTP server), it rewrites the existing Message-ID header with a new ID, but preserves the original Message-ID in the proprietary header "X-Microsoft-Original-Message-ID".

This bad design decision will have various bad effects, most obviously for message threading, but perhaps other places as well.

It seems that for the purpose of message threading, both the Message-ID and X-Microsoft-Original-Message-ID headers maybe should be considered.

Also, when replying to a message which contains both of these headers, they should probably both be copied into the References header, to help the recipient recognize the reply. The In-Reply-To header should probably use the Microsoft-regenerated Message-ID.

Of course, this is a Microsoft-created problem, but it seems like a few small program adjustments might help to work around it.

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other complaints about this problem:

https://answers.microsoft.com/en-us/outlook_com/forum/all/outlook-changes-the-custom-message-id-we-set-in/fe4f64dc-f97b-419d-a1ab-365a045426d0

https://learn.microsoft.com/en-us/answers/questions/1337178/custom-message-id-modified-by-the-outlook-smtp-ser