### 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)

ginstance->base_flags |= INSTANCE_DATA_FLAG_MULTIMESH_FORMAT_2D;
		}
		ginstance->base_flags |= INSTANCE_DATA_FLAG_MULTIMESH_HAS_COLOR;
		ginstance->base_flags |= INSTANCE_DATA_FLAG_MULTIMESH_HAS_CUSTOM_DATA;
		
		ginstance->base_flags |= (ginstance->trail_steps << INSTANCE_DATA_FLAGS_PARTICLE_TRAIL_SHIFT);
		if (!particles_storage->particles_is_using_local_coords(ginstance->data->base)) {
			store_transform = false;
		}
		ginstance->transforms_uniform_set = particles_storage->particles_get_instance_buffer_uniform_set(ginstance->data->base, scene_shader.default_shader_rd, TRANSFORMS_UNIFORM_SET);
		if (particles_storage->particles_get_frame_counter(ginstance->data->base) == 0) {
			
			particles_storage->update_particles();
		}
	} else if (ginstance->data->base_type == RS::INSTANCE_MESH) {
		if (mesh_storage->skeleton_is_valid(ginstance->data->skeleton)) {
			ginstance->transforms_uniform_set = mesh_storage->skeleton_get_3d_uniform_set(ginstance->data->skeleton, scene_shader.default_shader_rd, TRANSFORMS_UNIFORM_SET);
			if (ginstance->data->dirty_dependencies) {
				mesh_storage->skeleton_update_dependency(ginstance->data->skeleton, &ginstance->data->dependency_tracker);
			}
		}
	}
	ginstance->store_transform_cache = store_transform;
	if (ginstance->data->dirty_dependencies) {
		ginstance->data->dependency_tracker.update_end();
		ginstance->data->dirty_dependencies = false;
	}
	ginstance->dirty_list_element.remove_from_list();
}
void RenderForwardMobile::_update_dirty_geometry_instances() {