### 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_script->initializer) {
		return p_script->initializer;
	} else {
		GDScript *base_src = p_script->_base;
		if (base_src != nullptr) {
			return _super_constructor(base_src);
		} else {
			return nullptr;
		}
	}
}
void GDScript::_super_implicit_constructor(GDScript *p_script, GDScriptInstance *p_instance, Callable::CallError &r_error) {
	GDScript *base_src = p_script->_base;
	if (base_src != nullptr) {
		_super_implicit_constructor(base_src, p_instance, r_error);
		if (r_error.error != Callable::CallError::CALL_OK) {
			return;
		}
	}
	ERR_FAIL_NULL(p_script->implicit_initializer);
	p_script->implicit_initializer->call(p_instance, nullptr, 0, r_error);
}
GDScriptInstance *GDScript::_create_instance(const Variant **p_args, int p_argcount, Object *p_owner, bool p_is_ref_counted, Callable::CallError &r_error) {