### 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
docs.clear();
	doc = DocData::ClassDoc();
}
String GDScript::get_class_icon_path() const {
	return simplified_icon_path;
}
#endif
bool GDScript::_update_exports(bool *r_err, bool p_recursive_call, PlaceHolderScriptInstance *p_instance_to_update, bool p_base_exports_changed) {
#ifdef TOOLS_ENABLED
	static Vector<GDScript *> base_caches;
	if (!p_recursive_call) {
		base_caches.clear();
	}
	base_caches.append(this);
	bool changed = p_base_exports_changed;
	if (source_changed_cache) {
		source_changed_cache = false;
		changed = true;
		String basedir = path;
		if (basedir.is_empty()) {
			basedir = get_path();
		}
		if (!basedir.is_empty()) {
			basedir = basedir.get_base_dir();
		}
		GDScriptParser parser;
		GDScriptAnalyzer analyzer(&parser);
		Error err = parser.parse(source, path, false);
		if (err == OK && analyzer.analyze() == OK) {