### Godot version

4.0.1stable

### System information

Windows 11

### Issue description

I had a project that previously contained multiple folders, scripts, scenes, etc. However, I decided to delete everything except for a MeshInstance3D node and its associated script in order to start something new from that. The MeshInstance3D node has a material_overwrite property set with a shader material that was originally located in one of the folders I deleted carelessly.

Now, whenever I try to save the scene, the previously deleted "shader" folder reappears in the project directory. However, when I try to click on the folder, the entire project freezes before eventually crashing. 

I created a new project and attempted to attach a Shader Material, stored in a folder, to a MeshInstance3D node. I deleted the original folder that contained the shader material, and then saved the scene. The previously deleted folder did not reappear in the project directory, I was unable to reproduce the issue and I believe that the data stored in the scene is responsible for that behaviour. I have my own project folder that make it happen consistently which I'll join.

### Steps to reproduce

Just import the project and once it is opened, press "ctrl + s" to save, that will make a folder named "Shader" appear, if you click on that folder everything will freeze before eventually crashing.

### Minimal reproduction project

[reproduction_project.zip](https://github.com/godotengine/godot/files/11255484/reproduction_project.zip)

return true;
}
void Shader::_update_shader() const {
}
Array Shader::_get_shader_uniform_list(bool p_get_groups) {
	List<PropertyInfo> uniform_list;
	get_shader_uniform_list(&uniform_list, p_get_groups);
	Array ret;
	for (const PropertyInfo &pi : uniform_list) {
		ret.push_back(pi.operator Dictionary());
	}
	return ret;
}
void Shader::_bind_methods() {
	ClassDB::bind_method(D_METHOD("get_mode"), &Shader::get_mode);
	ClassDB::bind_method(D_METHOD("set_code", "code"), &Shader::set_code);
	ClassDB::bind_method(D_METHOD("get_code"), &Shader::get_code);
	ClassDB::bind_method(D_METHOD("set_default_texture_parameter", "name", "texture", "index"), &Shader::set_default_texture_parameter, DEFVAL(0));
	ClassDB::bind_method(D_METHOD("get_default_texture_parameter", "name", "index"), &Shader::get_default_texture_parameter, DEFVAL(0));
	ClassDB::bind_method(D_METHOD("get_shader_uniform_list", "get_groups"), &Shader::_get_shader_uniform_list, DEFVAL(false));
	ADD_PROPERTY(PropertyInfo(Variant::STRING, "code", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR), "set_code", "get_code");
	BIND_ENUM_CONSTANT(MODE_SPATIAL);
	BIND_ENUM_CONSTANT(MODE_CANVAS_ITEM);
	BIND_ENUM_CONSTANT(MODE_PARTICLES);
	BIND_ENUM_CONSTANT(MODE_SKY);
	BIND_ENUM_CONSTANT(MODE_FOG);
}
Shader::Shader() {