I added the following definitions to my init.el file, which seems to solve the problem:

(defun org-notmuch-search-open (path _)
  "Follow a notmuch search link specified by PATH."
  (notmuch-search path notmuch-search-oldest-first notmuch-search-hide-excluded))


(defun notmuch-search-default(path)
  "Add default options to notmuch-search"
  (notmuch-search path notmuch-search-oldest-first notmuch-search-hide-excluded))


> On May 21, 2024, at 6:32 AM, David Bremner <david@tethera.net> wrote:
> 
> erik colson <erik.colson@beavernet.be> writes:
> 
>> 
>> Thanks for the hint, but tried setting the var with setq-default, but
>> still same issue.. :
>> 
>>  notmuch-search-hide-excluded is a variable defined in ‘notmuch-lib.el’.
>> 
>>  Its value is nil
>>  Original value was t
>>  Local in buffer *notmuch-saved-tree-1week and unread*; global value is t
>> 
>>  Hide mail tagged with a excluded tag.
>> 
> 
> Hmm. I can't duplicate that here. Can you try with a minimal
> configuration? If you have the source you can run "./devel/try-emacs-mua
> -q" to run without any personal configuration.
> 
> Another thing to try is to hit "i" in a search view and see if it
> toggles properly.
> 
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