### 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
return "GDScript";
}
String GDScriptLanguage::get_extension() const {
	return "gd";
}
void GDScriptLanguage::finish() {
	_call_stack.free();
	
	GDScriptCache::clear();
	
	
	SelfList<GDScript> *s = script_list.first();
	while (s) {
		
		
		
		
		
		Ref<GDScript> scr = s->self();
		if (scr.is_valid()) {
			for (KeyValue<StringName, GDScriptFunction *> &E : scr->member_functions) {
				GDScriptFunction *func = E.value;
				for (int i = 0; i < func->argument_types.size(); i++) {
					func->argument_types.write[i].script_type_ref = Ref<Script>();
				}
				func->return_type.script_type_ref = Ref<Script>();
			}
			for (KeyValue<StringName, GDScript::MemberInfo> &E : scr->member_indices) {
				E.value.data_type.script_type_ref = Ref<Script>();
			}