### Godot version

v4.2.rc.mono.custom_build [ad72de508]

### System information

Windows 10

### Issue description

As I pointed out several times earlier in [#80284](https://github.com/godotengine/godot/pull/80284#issuecomment-1722120503), the references to singletons in `GDScript` are still not updated after the `GDExtension` reload.

https://github.com/godotengine/godot/assets/7782218/f90052a5-0de2-4310-8235-f0b9e2f74b3a

Singletons themselves are updated and work correctly, but references to these singletons are not updated in `@tool` scripts. That is, `Engine.get_singleton` returns the actual working reference, but using the singleton directly through its name causes errors.

### Steps to reproduce

* Clone `4.2.reload_singleton` branch from the MRP repository https://github.com/DmitriySalnikov/gde_test_cases/tree/4.2.reload_singleton
* Build as usual
* Open the project from the `project/` folder
* Add one character to the source code and rebuild
* Focus on the editor to reload extension
* Watch for error spam when calling by singleton name

### Minimal reproduction project

https://github.com/DmitriySalnikov/gde_test_cases/tree/4.2.reload_singleton
{
		MutexLock lock(mutex);
		SelfList<GDScript> *elem = script_list.first();
		while (elem) {
			GDScript *scr = elem->self();
			if (scr->fully_qualified_name == p_name) {
				return scr;
			}
			elem = elem->next();
		}
	}
	Ref<GDScript> scr;
	scr.instantiate();
	scr->fully_qualified_name = p_name;
	return scr;
}
Ref<Resource> ResourceFormatLoaderGDScript::load(const String &p_path, const String &p_original_path, Error *r_error, bool p_use_sub_threads, float *r_progress, CacheMode p_cache_mode) {
	Error err;
	Ref<GDScript> scr = GDScriptCache::get_full_script(p_path, err, "", p_cache_mode == CACHE_MODE_IGNORE);
	if (err && scr.is_valid()) {
		
		ERR_PRINT_ED(vformat(R"(Failed to load script "%s" with error "%s".)", p_path, error_names[err]));
	}
	if (r_error) {
		
		*r_error = scr.is_valid() ? OK : err;
	}
	return scr;
}
void ResourceFormatLoaderGDScript::get_recognized_extensions(List<String> *p_extensions) const {