### 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
if (p_members) {
		for (const StringName &E : members) {
			p_members->insert(E);
		}
	}
}
const Variant GDScript::get_rpc_config() const {
	return rpc_config;
}
void GDScript::unload_static() const {
	GDScriptCache::remove_script(fully_qualified_name);
}
Variant GDScript::callp(const StringName &p_method, const Variant **p_args, int p_argcount, Callable::CallError &r_error) {
	GDScript *top = this;
	while (top) {
		HashMap<StringName, GDScriptFunction *>::Iterator E = top->member_functions.find(p_method);
		if (E) {
			ERR_FAIL_COND_V_MSG(!E->value->is_static(), Variant(), "Can't call non-static function '" + String(p_method) + "' in script.");
			return E->value->call(nullptr, p_args, p_argcount, r_error);
		}
		top = top->_base;
	}
	
	return Script::callp(p_method, p_args, p_argcount, r_error);
}
bool GDScript::_get(const StringName &p_name, Variant &r_ret) const {