so...

I've taken a look at this file: /nix/store/22dzv5x7q98c890f67ilia4vwmhgxjzq-hm-dconf.ini

Which is referenced by /nix/store/rqyhp24x4cha7qx70i71rq0s32sd7hs1-home-manager-generation/activate:

$DRY_RUN_CMD $DCONF_DBUS_RUN_SESSION /nix/store/d9zam93fa4mj43fz3h09cajh81vgpqvn-dconf-0.40.0/bin/dconf load / < /nix/store/22dzv5x7q98c890f67ilia4vwmhgxjzq-hm-dconf.ini

It contains most of my custom settings, but where I have:

      "org/gnome/shell/keybindings" = {
        open-application-menu = [];
        toggle-overview = [];
        # Gnome tries to grab Super+m for this, the bastard
        toggle-message-tray = [ "<Super>v" ];
      };

It has:

$DRY_RUN_CMD $DCONF_DBUS_RUN_SESSION /nix/store/d9zam93fa4mj43fz3h09cajh81vgpqvn-dconf-0.40.0/bin/dconf load / < /nix/store/22dzv5x7q98c890f67ilia4vwmhgxjzq-hm-dconf.ini

so...

I've taken a look at this file: /nix/store/22dzv5x7q98c890f67ilia4vwmhgxjzq-hm-dconf.ini

Which is referenced by /nix/store/rqyhp24x4cha7qx70i71rq0s32sd7hs1-home-manager-generation/activate:

$DRY_RUN_CMD $DCONF_DBUS_RUN_SESSION /nix/store/d9zam93fa4mj43fz3h09cajh81vgpqvn-dconf-0.40.0/bin/dconf load / < /nix/store/22dzv5x7q98c890f67ilia4vwmhgxjzq-hm-dconf.ini

It contains most of my custom settings, but where I have:

      "org/gnome/shell/keybindings" = {
        open-application-menu = [];
        toggle-overview = [];
        # Gnome tries to grab Super+m for this, the bastard
        toggle-message-tray = [ "<Super>v" ];
      };

It has (in the generated INI file):

[org/gnome/shell/keybindings]
open-application-menu=@as []

In reply to @jtojnar:matrix.org
gnome-settings-daemon is the component responsible for managing keybindings. For example, I get Failed to grab accelerator for keybinding when I switch to a home-manager config with conflicts.

❯ journalctl -b | grep .gsd-media-keys
Jul 06 15:54:14 mifla .gsd-media-keys[1457]: Failed to grab accelerator for keybinding settings:playback-repeat
Jul 06 15:54:14 mifla .gsd-media-keys[1457]: Failed to grab accelerator for keybinding settings:hibernate
Jul 06 15:54:21 mifla .gsd-media-keys[1457]: Unable to get default sink
Jul 06 15:54:21 mifla .gsd-media-keys[1457]: Unable to get default source
Jul 06 15:54:23 mifla .gsd-media-keys[2483]: Failed to grab accelerator for keybinding settings:hibernate
Jul 06 15:54:23 mifla .gsd-media-keys[2483]: Failed to grab accelerator for keybinding settings:playback-repeat
Jul 06 15:54:23 mifla .gsd-media-keys[2483]: Failed to grab accelerator for keybinding settings:screensaver
Jul 06 15:54:23 mifla .gsd-media-keys[2483]: gvc_mixer_card_get_index: assertion 'GVC_IS_MIXER_CARD (card)' failed
Jul 06 15:54:34 mifla systemd[2065]: Started Application launched by gsd-media-keys.
Jul 06 15:59:33 mifla systemd[2065]: Started Application launched by gsd-media-keys.
Jul 06 15:59:43 mifla systemd[2065]: Started Application launched by gsd-media-keys.
Jul 06 16:01:45 mifla systemd[2065]: Started Application launched by gsd-media-keys.
Jul 06 16:08:36 mifla systemd[2065]: Started Application launched by gsd-media-keys.
Jul 06 16:15:02 mifla systemd[2065]: Started Application launched by gsd-media-keys.

Okay so nixos-rebuild --switch as ever restores my keys. Finding activate script:

systemctl show home-manager-silas.service | grep Exec

❯ cat activate | grep dconf
_iNote "Activating %s" "dconfSettings"
  /nix/store/83mizl0zb58zzyby47rk7iafa1mrrrmr-dconf-cleanup \
    "$oldGenPath/state/dconf-keys.json" \
    "$newGenPath/state/dconf-keys.json"
$DRY_RUN_CMD $DCONF_DBUS_RUN_SESSION /nix/store/bll3yc6g3fc6bgxrs97idjxx27qkn9n2-dconf-0.40.0/bin/dconf load / < /nix/store/6676vj0l7kawrqkblqqicyjl3gc99im6-hm-dconf.ini

Now my settings are back:

[org/gnome/shell/keybindings]
open-application-menu=@as []
toggle-message-tray=@as ['<Super>v']
toggle-overview=@as []

After restart, broken:

❯ systemctl show home-manager-silas.service | grep ExecStart=
ExecStart={ path=/nix/store/fqhlc4pka1a9yx5dfy392abxlkibf9hv-hm-setup-env ; argv[]=/nix/store/fqhlc4pka1a9yx5dfy392abxlkibf9hv-hm-setup-env /nix/store/rqyhp24x4cha7qx70i71rq0s32sd7hs1-home-manager-generation ; ignore_errors=no ; start_time=[Thu 2023-07-06 16:18:51 CEST] ; stop_time=[Thu 2023-07-06 16:18:52 CEST] ; pid=941 ; code=exited ; status=0 }

After nixos-rebuild --switch (working):

❯ systemctl show home-manager-silas.service | grep ExecStart=
ExecStart={ path=/nix/store/dpalk76wpvnyfhnr2byxmhnpxrimbal7-hm-setup-env ; argv[]=/nix/store/dpalk76wpvnyfhnr2byxmhnpxrimbal7-hm-setup-env /nix/store/b4pclvgfkw8q6rvpir9zh28dms149br4-home-manager-generation ; ignore_errors=no ; start_time=[Thu 2023-07-06 16:22:06 CEST] ; stop_time=[Thu 2023-07-06 16:22:07 CEST] ; pid=5368 ; code=exited ; status=0 }