### Godot version

v4.1.dev4.mono.official [5c2295ff5]

### System information

Godot v4.1.dev4.mono - Windows 10.0.19045 - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1660 Ti with Max-Q Design (NVIDIA; 31.0.15.3179) - Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz (12 Threads)

### Issue description

When I open my project console gets filled with these errors.

```
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: Condition "skeleton->size == 0" is true. Returning: RID()
   at: skeleton_get_3d_uniform_set (./servers/rendering/renderer_rd/storage_rd/mesh_storage.h:693)
ERROR: Condition "skeleton->size == 0" is true. Returning: RID()
   at: skeleton_get_3d_uniform_set (./servers/rendering/renderer_rd/storage_rd/mesh_storage.h:693)
```
### Steps to reproduce (from fresh new project)
Steps to reproduce `ERROR: Condition "skeleton->size == 0" is true. Returning: RID()` error.
1. Create new project.
1.1 Godot version used: v4.1.beta2.mono.official [a2575cba4]).
1.2 I have this setting On: Editor -> Editor Settings -> General -> Interface -> Scene Tabs -> "Restore Scenes On Load".
2. Copy/Paste .glb model with a skeleton to the project folder.
3. Double click .glb file in the editor and click Reimport.
4. Right click .glb file and select New Inherited Scene.
5. Click ctrl+s to save that scene for example player.tscn.
6. Right click player.tscn and select Instantiate.
7. Save everything and restart Godot editor. When launching editor you will see message `ERROR: Condition "skeleton->size == 0" is true. Returning: RID()` in console and Output.

### Steps to reproduce (from MRP)

Open project

### Minimal reproduction project

MRP uses v4.1.beta1.mono.official [828ec2c5d], but same error still persists
[MRP.zip](https://github.com/godotengine/godot/files/11703993/MRP.zip)

}
	if (render_cubemap) {
		
		_render_shadow_append(render_fb, p_instances, light_projection, light_transform, zfar, 0, 0, reverse_cull_face, false, false, use_pancake, p_camera_plane, p_lod_distance_multiplier, p_screen_mesh_lod_threshold, Rect2(), false, true, true, true, p_render_info);
		if (finalize_cubemap) {
			_render_shadow_process();
			_render_shadow_end();
			
			Rect2 atlas_rect_norm = atlas_rect;
			atlas_rect_norm.position /= float(atlas_size);
			atlas_rect_norm.size /= float(atlas_size);
			copy_effects->copy_cubemap_to_dp(render_texture, atlas_fb, atlas_rect_norm, atlas_rect.size, light_projection.get_z_near(), light_projection.get_z_far(), false);
			atlas_rect_norm.position += Vector2(dual_paraboloid_offset) * atlas_rect_norm.size;
			copy_effects->copy_cubemap_to_dp(render_texture, atlas_fb, atlas_rect_norm, atlas_rect.size, light_projection.get_z_near(), light_projection.get_z_far(), true);
			
			light_storage->light_instance_set_shadow_transform(p_light, Projection(), light_storage->light_instance_get_base_transform(p_light), zfar, 0, 0, 0);
		}
	} else {
		
		_render_shadow_append(render_fb, p_instances, light_projection, light_transform, zfar, 0, 0, reverse_cull_face, using_dual_paraboloid, using_dual_paraboloid_flip, use_pancake, p_camera_plane, p_lod_distance_multiplier, p_screen_mesh_lod_threshold, atlas_rect, flip_y, p_clear_region, p_open_pass, p_close_pass, p_render_info);
	}
}
void RenderForwardClustered::_render_shadow_begin() {
	scene_state.shadow_passes.clear();
	RD::get_singleton()->draw_command_begin_label("Shadow Setup");
	_update_render_base_uniform_set();
	render_list[RENDER_LIST_SECONDARY].clear();
	scene_state.instance_data[RENDER_LIST_SECONDARY].clear();
}
void RenderForwardClustered::_render_shadow_append(RID p_framebuffer, const PagedArray<RenderGeometryInstance *> &p_instances, const Projection &p_projection, const Transform3D &p_transform, float p_zfar, float p_bias, float p_normal_bias, bool p_reverse_cull_face, bool p_use_dp, bool p_use_dp_flip, bool p_use_pancake, const Plane &p_camera_plane, float p_lod_distance_multiplier, float p_screen_mesh_lod_threshold, const Rect2i &p_rect, bool p_flip_y, bool p_clear_region, bool p_begin, bool p_end, RenderingMethod::RenderInfo *p_render_info) {