This patch series does some fixes and improvements for hiding and showing messages in notmuch-show. However it comes with a regression: isearch is broken for hidden overlays when `invisible' property is a list. I have opened emacs bug #8721 [1] and sent a patch. It has been committed to emacs trunk r104356.
I do not know if this should be pushed or wait until emacs with the fix is released. Regards, Dmitry [1] http://debbugs.gnu.org/cgi/bugreport.cgi?bug=8721
