### 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)

for (uint32_t i = 0; i < p_render_data->directional_shadows.size(); i++) {
			_render_shadow_pass(p_render_data->render_shadows[p_render_data->directional_shadows[i]].light, p_render_data->shadow_atlas, p_render_data->render_shadows[p_render_data->directional_shadows[i]].pass, p_render_data->render_shadows[p_render_data->directional_shadows[i]].instances, camera_plane, lod_distance_multiplier, p_render_data->scene_data->screen_mesh_lod_threshold, false, i == p_render_data->directional_shadows.size() - 1, false, p_render_data->render_info);
		}
		
		for (uint32_t i = 0; i < p_render_data->shadows.size(); i++) {
			_render_shadow_pass(p_render_data->render_shadows[p_render_data->shadows[i]].light, p_render_data->shadow_atlas, p_render_data->render_shadows[p_render_data->shadows[i]].pass, p_render_data->render_shadows[p_render_data->shadows[i]].instances, camera_plane, lod_distance_multiplier, p_render_data->scene_data->screen_mesh_lod_threshold, i == 0, i == p_render_data->shadows.size() - 1, true, p_render_data->render_info);
		}
		_render_shadow_process();
	}
	
	if (render_gi) {
		gi.process_gi(rb, p_normal_roughness_slices, p_voxel_gi_buffer, p_render_data->environment, p_render_data->scene_data->view_count, p_render_data->scene_data->view_projection, p_render_data->scene_data->view_eye_offset, p_render_data->scene_data->cam_transform, *p_render_data->voxel_gi_instances);
	}
	
	if (render_shadows) {
		_render_shadow_end(RD::BARRIER_MASK_NO_BARRIER);
	}
	if (render_gi) {
		RD::get_singleton()->compute_list_end(RD::BARRIER_MASK_NO_BARRIER); 
	}
	if (rb_data.is_valid() && ss_effects) {
		
		
		
		if (p_use_ssao || p_use_ssil) {
			
			for (uint32_t v = 0; v < rb->get_view_count(); v++) {
				ss_effects->downsample_depth(rb, v, p_render_data->scene_data->view_projection[v]);
			}
			if (p_use_ssao) {