### 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 script;
}
ScriptLanguage *GDScriptInstance::get_language() {
	return GDScriptLanguage::get_singleton();
}
const Variant GDScriptInstance::get_rpc_config() const {
	return script->get_rpc_config();
}
void GDScriptInstance::reload_members() {
#ifdef DEBUG_ENABLED
	Vector<Variant> new_members;
	new_members.resize(script->member_indices.size());
	
	for (KeyValue<StringName, GDScript::MemberInfo> &E : script->member_indices) {
		if (member_indices_cache.has(E.key)) {
			Variant value = members[member_indices_cache[E.key]];
			new_members.write[E.value.index] = value;
		}
	}
	members.resize(new_members.size()); 
	
	members = new_members;
	
	member_indices_cache.clear();
	for (const KeyValue<StringName, GDScript::MemberInfo> &E : script->member_indices) {
		member_indices_cache[E.key] = E.value.index;
	}
#endif
}
GDScriptInstance::GDScriptInstance() {