### 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 (has_method(CoreStringNames::get_singleton()->_to_string)) {
		Callable::CallError ce;
		Variant ret = callp(CoreStringNames::get_singleton()->_to_string, nullptr, 0, ce);
		if (ce.error == Callable::CallError::CALL_OK) {
			if (ret.get_type() != Variant::STRING) {
				if (r_valid) {
					*r_valid = false;
				}
				ERR_FAIL_V_MSG(String(), "Wrong type for " + CoreStringNames::get_singleton()->_to_string + ", must be a String.");
			}
			if (r_valid) {
				*r_valid = true;
			}
			return ret.operator String();
		}
	}
	if (r_valid) {
		*r_valid = false;
	}
	return String();
}
Ref<Script> GDScriptInstance::get_script() const {