This bug was recently discussed on the mailing list:
id:878wdifu13.fsf@yoom.home.cworth.org
so note one idea for fixing it.
notmuch command-line tool
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+Fix "notmuch show" so that the UI doesn't fail to show a thread that
+is visible in a search buffer, but happens to no longer match the
+current search. (Perhaps add a --matching=<secondary-search-terms>
+option (or similar) to "notmuch show".)
+
Teach "notmuch search" to return many different kinds of results. Some
ideas: