### 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)

} else {
		
		light_storage->update_reflection_probe_buffer(p_render_data, *p_render_data->reflection_probes, p_render_data->scene_data->cam_transform.affine_inverse(), p_render_data->environment);
	}
	uint32_t directional_light_count = 0;
	uint32_t positional_light_count = 0;
	light_storage->update_light_buffers(p_render_data, *p_render_data->lights, p_render_data->scene_data->cam_transform, p_render_data->shadow_atlas, using_shadows, directional_light_count, positional_light_count, p_render_data->directional_light_soft_shadows);
	texture_storage->update_decal_buffer(*p_render_data->decals, p_render_data->scene_data->cam_transform);
	p_render_data->directional_light_count = directional_light_count;
}
void RenderForwardMobile::_render_scene(RenderDataRD *p_render_data, const Color &p_default_bg_color) {
	RendererRD::LightStorage *light_storage = RendererRD::LightStorage::get_singleton();
	ERR_FAIL_NULL(p_render_data);
	Ref<RenderSceneBuffersRD> rb = p_render_data->render_buffers;
	ERR_FAIL_COND(rb.is_null());
	Ref<RenderBufferDataForwardMobile> rb_data;
	if (rb->has_custom_data(RB_SCOPE_MOBILE)) {
		
		
		rb_data = rb->get_custom_data(RB_SCOPE_MOBILE);
	}
	bool is_reflection_probe = p_render_data->reflection_probe.is_valid();
	RENDER_TIMESTAMP("Prepare 3D Scene");
	_update_vrs(rb);
	RENDER_TIMESTAMP("Setup 3D Scene");
	/* TODO
	// check if we need motion vectors
	if (get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_MOTION_VECTORS) {
		p_render_data->scene_data->calculate_motion_vectors = true;
	} else if (render target has velocity override) { // TODO