Yeah, apparently `kill-emacs' is considered "low-level primitive":

    Functions to call with no arguments to query about killing Emacs.
    If any of these functions returns nil, killing Emacs is canceled.
    ‘save-buffers-kill-emacs’ calls these functions, but ‘kill-emacs’,
    the low level primitive, does not.  See also ‘kill-emacs-hook’.

Since I have rebound C-x C-c for my private use (why waste such a nice
shortcut on something used once in a few days?), I have been using
`kill-emacs'. But apparently it's not what should be used... Emacs making
it easy to silently break things, nothing new.

I suggest that `desktop-release-lock' call is still moved from something
hooked on `kill-emacs-query-functions' to `kill-emacs-hook'. That part is
supposed to be done unconditionally.

Paul

On Wed, 27 Jul 2022 at 19:32, Eli Zaretskii <eliz@gnu.org> wrote:

> > From: Paul Pogonyshev <pogonyshev@gmail.com>
> > Date: Wed, 27 Jul 2022 18:58:36 +0200
> > Cc: 56800@debbugs.gnu.org
> >
> > But why does even cleanly exiting Emacs leave desktop file "apparently
> used"?
>
> It shouldn't, and it doesn't here.  Something I hope you will look
> into and tell what you found.
>