### 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)

scene_data.screen_mesh_lod_threshold = p_screen_mesh_lod_threshold;
	}
	PassMode pass_mode = p_use_dp ? PASS_MODE_SHADOW_DP : PASS_MODE_SHADOW;
	uint32_t render_list_from = render_list[RENDER_LIST_SECONDARY].elements.size();
	_fill_render_list(RENDER_LIST_SECONDARY, &render_data, pass_mode, true);
	uint32_t render_list_size = render_list[RENDER_LIST_SECONDARY].elements.size() - render_list_from;
	render_list[RENDER_LIST_SECONDARY].sort_by_key_range(render_list_from, render_list_size);
	_fill_element_info(RENDER_LIST_SECONDARY, render_list_from, render_list_size);
	{
		
		bool flip_cull = p_use_dp_flip;
		if (p_flip_y) {
			flip_cull = !flip_cull;
		}
		shadow_pass.element_from = render_list_from;
		shadow_pass.element_count = render_list_size;
		shadow_pass.flip_cull = flip_cull;
		shadow_pass.pass_mode = pass_mode;
		shadow_pass.rp_uniform_set = RID(); 
		shadow_pass.camera_plane = p_camera_plane;
		shadow_pass.screen_mesh_lod_threshold = scene_data.screen_mesh_lod_threshold;
		shadow_pass.lod_distance_multiplier = scene_data.lod_distance_multiplier;
		shadow_pass.framebuffer = p_framebuffer;
		shadow_pass.initial_depth_action = p_begin ? (p_clear_region ? RD::INITIAL_ACTION_CLEAR_REGION : RD::INITIAL_ACTION_CLEAR) : (p_clear_region ? RD::INITIAL_ACTION_CLEAR_REGION_CONTINUE : RD::INITIAL_ACTION_CONTINUE);
		shadow_pass.final_depth_action = p_end ? RD::FINAL_ACTION_READ : RD::FINAL_ACTION_CONTINUE;
		shadow_pass.rect = p_rect;
		scene_state.shadow_passes.push_back(shadow_pass);
	}
}
void RenderForwardMobile::_render_shadow_process() {