### 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)

resolve_effects->resolve_depth(rb_data->get_depth_msaa(v), rb->get_depth_texture(v), rb->get_internal_size(), texture_multisamples[rb->get_msaa_3d()]);
			}
		}
	}
	if (using_separate_specular) {
		if (using_sss) {
			RENDER_TIMESTAMP("Sub-Surface Scattering");
			RD::get_singleton()->draw_command_begin_label("Process Sub-Surface Scattering");
			_process_sss(rb, p_render_data->scene_data->cam_projection);
			RD::get_singleton()->draw_command_end_label();
		}
		if (using_ssr) {
			RENDER_TIMESTAMP("Screen-Space Reflections");
			RD::get_singleton()->draw_command_begin_label("Process Screen-Space Reflections");
			RID specular_views[RendererSceneRender::MAX_RENDER_VIEWS];
			for (uint32_t v = 0; v < p_render_data->scene_data->view_count; v++) {
				specular_views[v] = rb_data->get_specular(v);
			}
			_process_ssr(rb, color_only_framebuffer, normal_roughness_views, rb_data->get_specular(), specular_views, p_render_data->environment, p_render_data->scene_data->view_projection, p_render_data->scene_data->view_eye_offset, rb->get_msaa_3d() == RS::VIEWPORT_MSAA_DISABLED);
			RD::get_singleton()->draw_command_end_label();
		} else {
			
			RENDER_TIMESTAMP("Merge Specular");
			copy_effects->merge_specular(color_only_framebuffer, rb_data->get_specular(), rb->get_msaa_3d() == RS::VIEWPORT_MSAA_DISABLED ? RID() : rb->get_internal_texture(), RID(), p_render_data->scene_data->view_count);
		}
	}
	if (scene_state.used_screen_texture) {
		RENDER_TIMESTAMP("Copy Screen Texture");
		
		_render_buffers_copy_screen_texture(p_render_data);