The behavior was changed in commit
4aff2ca55bfe285ced36e9fe02c907d8b4120672
to affect all messages in the thread (and not only those matching
the current search) but the documentation was not updated (until
now).
(defun notmuch-search-remove-tag (tag)
"Remove a tag from the currently selected thread.
-The tag is removed from messages in the currently selected thread
-which match the current search terms."
+The tag is removed from all messages in the currently selected thread."
(interactive
(list (notmuch-select-tag-with-completion "Tag to remove: " (notmuch-search-find-thread-id))))
(notmuch-call-notmuch-process "tag" (concat "-" tag) (notmuch-search-find-thread-id))