How to manually set the "In-Reply-To" header in Thunderbird?

As mirh hinted in the comments of Luca’s answer, it seems Thunderbird will throw out the In-Reply-To header value unless the message ID is surrounded in angle brackets.

So, instead of choosing In-Reply-To: as a header and entering the value [email protected], instead use the value <[email protected]>.

I tested this on a Mailman list, and after additionally setting CC: to the mailing list email, my message was threaded properly in the list.

I was also bit by this same problem. I have then tried the header-tools-lite extension that can be used to edit the header of email messages. I created a new message, saved it as draft, edited the header (References field) and finally sent the message. It seems to work fine.

comment 1189889/1098266 mentions using Header Tools Lite. This is an old XUL extension and no longer will work with Thunderbird 68+, developer says on their website:

On the spotlight - END OF DEVELOPMENT AND SUPPORT

As is well known, Mozilla has chosen to renounce XUL/XPCOM based technology for extensions and has decided to replace it with Webextensions.

For non-experts, this means that extensions now use a completely different technology and that all "old style" extensions must be rewritten from scratch to work.

Not having enough time and motivation for such a complicated job, as well as for personal reasons, I decided to completely end the development and support of all my extensions.

There is this alternative however, which is how I do it:

Borrowed from MozillaZine: Custom headers. Archive link 1, 2. Just in case it disappears.

1. Check the value of: mail.identity.idX.useremail to determine which index number refers to your email account. ie Edit → Preferences → Advanced → General → Config Editor
2. Set user_pref("mail.identity.id1.headers", "References, InReplyTo"); to create the custom headers.
3. Change the custom headers, you could use a user.js for this.
4. Set the values for References, you can use as many References as you like, just make sure they are separated with a new-line character and a space ie: \n. user_pref("mail.identity.id1.header.References", "References: <[email protected]>\n <[email protected]>");
5. Set the In-Reply-To: ie user_pref("mail.identity.id1.header.InReplyTo", "In-Reply-To: <[email protected]>");
6. Restart Thunderbird and send your email.
7. Comment out the above set options in your user.js with /* */. Go back into about:config ie (Edit → Preferences → Advanced → General → Config Editor) and rightclick on the keys mail.identity.id1.headers, mail.identity.id1.header.References and mail.identity.id1.header.InReplyTo and click Reset. Do not set these values to anything else in a user.js, because it will interfere with Thunderbird's normal behavior when you click Reply on an email.