diff --git a/docs/changelog.rst b/docs/changelog.rst
index 79eca2514..0c7281c97 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -170,6 +170,9 @@ Detailed list of changes
 - Fix rendering of underlines when using larger text sizes with the space and
   en-space characters (:iss:`8950`)
 
+- Fix updating panel configuration on visibility toggle and via remote control
+  not working (:iss:`8984`)
+
 - Wayland: Update bundled copy of libwayland to 1.24 from 1.23.1 because the
   just released mesa 25.2.0 breaks with libwayland < 1.24 (:iss:`8884`)
 
diff --git a/kittens/panel/main.py b/kittens/panel/main.py
index 6f2ac90b5..3814f2500 100644
--- a/kittens/panel/main.py
+++ b/kittens/panel/main.py
@@ -25,6 +25,7 @@ from kitty.fast_data_types import (
     GLFW_LAYER_SHELL_OVERLAY,
     GLFW_LAYER_SHELL_PANEL,
     GLFW_LAYER_SHELL_TOP,
+    layer_shell_config_for_os_window,
     set_layer_shell_config,
     toggle_os_window_visibility,
 )
@@ -110,7 +111,6 @@ def have_config_files_been_updated(config_files: Iterable[str]) -> bool:
 def handle_single_instance_command(boss: BossType, sys_args: Sequence[str], environ: Mapping[str, str], notify_on_os_window_death: str | None = '') -> None:
     global args
     from kitty.cli import parse_override
-    from kitty.main import run_app
     from kitty.tabs import SpecialWindow
     try:
         new_args, items = parse_panel_args(list(sys_args[1:]))
@@ -118,17 +118,17 @@ def handle_single_instance_command(boss: BossType, sys_args: Sequence[str], envi
         log_error(f'Invalid arguments received over single instance socket: {sys_args} with error: {e}')
         return
     lsc = layer_shell_config(new_args)
-    layer_shell_config_changed = lsc != run_app.layer_shell_config
     config_changed = have_config_files_been_updated(new_args.config) or args.config != new_args.config or args.override != new_args.override
     args = new_args
     if config_changed:
         boss.load_config_file(*args.config, overrides=tuple(map(parse_override, new_args.override)))
     if args.toggle_visibility and boss.os_window_map:
         for os_window_id in boss.os_window_map:
+            existing = layer_shell_config_for_os_window(os_window_id)
+            layer_shell_config_changed = not existing or any(f for f in lsc._fields if getattr(lsc, f) != existing.get(f))
             toggle_os_window_visibility(os_window_id)
             if layer_shell_config_changed:
                 set_layer_shell_config(os_window_id, lsc)
-                run_app.layer_shell_config = lsc
         return
     items = items or [kitten_exe(), 'run-shell']
     os_window_id = boss.add_os_panel(lsc, args.cls, args.name)
diff --git a/kitty/glfw.c b/kitty/glfw.c
index 6eedc8679..48a658a16 100644
--- a/kitty/glfw.c
+++ b/kitty/glfw.c
@@ -2566,18 +2566,12 @@ toggle_os_window_visibility(PyObject *self UNUSED, PyObject *args) {
 static PyObject*
 layer_shell_config_for_os_window(PyObject *self UNUSED, PyObject *wid) {
     if (!PyLong_Check(wid)) { PyErr_SetString(PyExc_TypeError, "os_window_id must be a int"); return NULL; }
-#ifdef __APPLE__
-    (void)layer_shell_config_to_python;
-    Py_RETURN_NONE;
-#else
-    if (!global_state.is_wayland) Py_RETURN_NONE;
     id_type id = PyLong_AsUnsignedLongLong(wid);
     OSWindow *w = os_window_for_id(id);
     if (!w || !w->handle) Py_RETURN_NONE;
     const GLFWLayerShellConfig *c = glfwGetLayerShellConfig(w->handle);
     if (!c) Py_RETURN_NONE;
     return layer_shell_config_to_python(c);
-#endif
 }
 
 static PyObject*