Quoth Aaron Ecay on Jan 08 at  7:56 pm:
> On Thu, 05 Jan 2012 22:32:16 +0200, Jani Nikula <jani@nikula.org> wrote:
> 
> [...]
> 
> > In the show view it only modifies the messages that are currently
> > visible. This is to make sure you don't accidentally archive things that
> > have arrived after refreshing the buffer. I think this is safest.
> 
> Hmm.  Perhaps it would make sense to add a check in the search view that
> the thread being archived[1] has the same number of messages as it did
> when the buffer was constructed.  (The information on how many messages
> the thread has is in the buffer; we would then compare this to the result
> of “notmuch count thread:000foo” when the user requests to archive.)  If
> the counts don’t match, the interface should show a message in the echo
> area and (probably) refuse to do the tagging.

That sounds like a clever workaround.

There's been quite a bit of discussion on fixing this properly.  See,
for example
id:"CAH-f9WsPj=1Eu=g3sOePJgCTBFs6HrLdLq18xMEnJ8aZ00yCEg@mail.gmail.com".
The gist is that we need to include message IDs (or document IDs) in
the search output and use these in tagging operations, rather than the
unstable thread:XXX queries.  Unfortunately, actually fixing this got
stalled since adding this information the text format is a fool's
errand (having been the fool, I can say this!), so we need to switch
Emacs over to using the JSON search format first.  However, once
that's done, it's a relatively simple change.