### 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)

ss_effects->sss_set_quality(p_quality);
}
void RenderForwardClustered::sub_surface_scattering_set_scale(float p_scale, float p_depth_scale) {
	ss_effects->sss_set_scale(p_scale, p_depth_scale);
}
RenderForwardClustered *RenderForwardClustered::singleton = nullptr;
void RenderForwardClustered::sdfgi_update(const Ref<RenderSceneBuffers> &p_render_buffers, RID p_environment, const Vector3 &p_world_position) {
	Ref<RenderSceneBuffersRD> rb = p_render_buffers;
	ERR_FAIL_COND(rb.is_null());
	Ref<RendererRD::GI::SDFGI> sdfgi;
	if (rb->has_custom_data(RB_SCOPE_SDFGI)) {
		sdfgi = rb->get_custom_data(RB_SCOPE_SDFGI);
	}
	bool needs_sdfgi = p_environment.is_valid() && environment_get_sdfgi_enabled(p_environment);
	if (!needs_sdfgi) {
		if (sdfgi.is_valid()) {
			
			sdfgi.unref();
			rb->set_custom_data(RB_SCOPE_SDFGI, sdfgi);
		}
		return;
	}
	static const uint32_t history_frames_to_converge[RS::ENV_SDFGI_CONVERGE_MAX] = { 5, 10, 15, 20, 25, 30 };
	uint32_t requested_history_size = history_frames_to_converge[gi.sdfgi_frames_to_converge];
	if (sdfgi.is_valid() && (sdfgi->num_cascades != environment_get_sdfgi_cascades(p_environment) || sdfgi->min_cell_size != environment_get_sdfgi_min_cell_size(p_environment) || requested_history_size != sdfgi->history_size || sdfgi->uses_occlusion != environment_get_sdfgi_use_occlusion(p_environment) || sdfgi->y_scale_mode != environment_get_sdfgi_y_scale(p_environment))) {
		
		sdfgi.unref();
		rb->set_custom_data(RB_SCOPE_SDFGI, sdfgi);
	}
	if (sdfgi.is_null()) {