### 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 (!path_valid && !get_path().is_empty()) {
		return get_path();
	}
	return path;
}
Error GDScript::load_source_code(const String &p_path) {
	if (p_path.is_empty() || p_path.begins_with("gdscript://") || ResourceLoader::get_resource_type(p_path.get_slice("::", 0)) == "PackedScene") {
		return OK;
	}
	Vector<uint8_t> sourcef;
	Error err;
	Ref<FileAccess> f = FileAccess::open(p_path, FileAccess::READ, &err);
	if (err) {
		const char *err_name;
		if (err < 0 || err >= ERR_MAX) {
			err_name = "(invalid error code)";
		} else {
			err_name = error_names[err];
		}
		ERR_FAIL_COND_V_MSG(err, err, "Attempt to open script '" + p_path + "' resulted in error '" + err_name + "'.");
	}
	uint64_t len = f->get_length();
	sourcef.resize(len + 1);