### 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)

if (scene_state.instance_data[p_render_list].size() > 0) {
		if (scene_state.instance_buffer[p_render_list] == RID() || scene_state.instance_buffer_size[p_render_list] < scene_state.instance_data[p_render_list].size()) {
			if (scene_state.instance_buffer[p_render_list] != RID()) {
				RD::get_singleton()->free(scene_state.instance_buffer[p_render_list]);
			}
			uint32_t new_size = nearest_power_of_2_templated(MAX(uint64_t(INSTANCE_DATA_BUFFER_MIN_SIZE), scene_state.instance_data[p_render_list].size()));
			scene_state.instance_buffer[p_render_list] = RD::get_singleton()->storage_buffer_create(new_size * sizeof(SceneState::InstanceData));
			scene_state.instance_buffer_size[p_render_list] = new_size;
		}
		RD::get_singleton()->buffer_update(scene_state.instance_buffer[p_render_list], 0, sizeof(SceneState::InstanceData) * scene_state.instance_data[p_render_list].size(), scene_state.instance_data[p_render_list].ptr(), RD::BARRIER_MASK_RASTER);
	}
}
void RenderForwardClustered::_fill_instance_data(RenderListType p_render_list, int *p_render_info, uint32_t p_offset, int32_t p_max_elements, bool p_update_buffer) {
	RenderList *rl = &render_list[p_render_list];
	uint32_t element_total = p_max_elements >= 0 ? uint32_t(p_max_elements) : rl->elements.size();
	scene_state.instance_data[p_render_list].resize(p_offset + element_total);
	rl->element_info.resize(p_offset + element_total);
	if (p_render_info) {
		p_render_info[RS::VIEWPORT_RENDER_INFO_OBJECTS_IN_FRAME] += element_total;
	}
	uint64_t frame = RSG::rasterizer->get_frame_number();
	uint32_t repeats = 0;
	GeometryInstanceSurfaceDataCache *prev_surface = nullptr;
	for (uint32_t i = 0; i < element_total; i++) {
		GeometryInstanceSurfaceDataCache *surface = rl->elements[i + p_offset];
		GeometryInstanceForwardClustered *inst = surface->owner;
		SceneState::InstanceData &instance_data = scene_state.instance_data[p_render_list][i + p_offset];
		if (inst->prev_transform_dirty && frame > inst->prev_transform_change_frame + 1 && inst->prev_transform_change_frame) {
			inst->prev_transform = inst->transform;
			inst->prev_transform_dirty = false;