Thanks for these ideas.

It turns out it was a isync-mutt integration issue on my side. Now this
macro works as expected:

macro index 0 "!mbsync email:INBOX && notmuch
new<enter><change-folder>=inbox<enter>"

One needs to change to the current folder to get everything re-read by
mutt. Otherwise, the "Mailbox is unchanged" issue pops up. Oddly, if one
doesn't invoke change-folder deletion is detected, but sync-folder ($)
refuses to remove messages. It's also a bit counterintuitive sync-folder
($) is only a one way sync.

On Sat, Feb 6, 2016 at 9:31 AM, Evgeniy Berdnikov <b...@protva.ru> wrote:

> On Sat, Feb 06, 2016 at 02:55:57AM +0000, Gammel Holte wrote:
> > If one of the messages in my local inbox is marked as deleted by syncing
> > with the remote server (getting the tag D in mutt), I cannot make it
> > disappear using the sync-mailbox command ($). Attempts to do so lead to a
> > "Mailbox is unchanged" message.
>
>  Probably Mutt checks for modification time of mailbox and compares it
>  with time of last user's delete command. If so, this situation may be
>  considered as Mutt's bug.
>
>  Try this workarond: start edition of any deleted message with "e", make
>  some changes (to create new version of message), exit editor, mark new
>  message as deleted (d) and resync ($). If it works, try to make keyboard
>  binding to some external command, which updates time stamps on mailbox
>  folder (via "touch", eg). It could give a hint to Mutt that mailbox was
>  changed.
> --
>  Eugene Berdnikov
>
>
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