### 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
#ifdef TOOLS_ENABLED
	PlaceHolderScriptInstance *si = memnew(PlaceHolderScriptInstance(GDScriptLanguage::get_singleton(), Ref<Script>(this), p_this));
	placeholders.insert(si);
	_update_exports(nullptr, false, si);
	return si;
#else
	return nullptr;
#endif
}
bool GDScript::instance_has(const Object *p_this) const {
	MutexLock lock(GDScriptLanguage::singleton->mutex);
	return instances.has((Object *)p_this);
}
bool GDScript::has_source_code() const {
	return !source.is_empty();
}
String GDScript::get_source_code() const {
	return source;
}
void GDScript::set_source_code(const String &p_code) {
	if (source == p_code) {
		return;
	}
	source = p_code;
#ifdef TOOLS_ENABLED
	source_changed_cache = true;
#endif
}
#ifdef TOOLS_ENABLED
void GDScript::_update_exports_values(HashMap<StringName, Variant> &values, List<PropertyInfo> &propnames) {