Ico Doornekamp <notmuch@zevv.nl> writes:

>
> I tried to remove the "References" and "In-Reply-To" headers of the
> offending mail, and reindex the thread. This seems not enough to
> convince notmuch that these mails are no longer related, because the
> original and separated thread still end up with the same thread ID.
>

I would expect that to work in general.

One possibility is there are duplicate files for the message.

I'm reminded that I meant to distribute the attached script somewhere
(either in notmuch or in mailscripts). Perhaps you can run it before and
after your edits.