### 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
p_extensions->push_back("gd");
}
bool ResourceFormatLoaderGDScript::handles_type(const String &p_type) const {
	return (p_type == "Script" || p_type == "GDScript");
}
String ResourceFormatLoaderGDScript::get_resource_type(const String &p_path) const {
	String el = p_path.get_extension().to_lower();
	if (el == "gd") {
		return "GDScript";
	}
	return "";
}
void ResourceFormatLoaderGDScript::get_dependencies(const String &p_path, List<String> *p_dependencies, bool p_add_types) {
	Ref<FileAccess> file = FileAccess::open(p_path, FileAccess::READ);
	ERR_FAIL_COND_MSG(file.is_null(), "Cannot open file '" + p_path + "'.");
	String source = file->get_as_utf8_string();
	if (source.is_empty()) {
		return;
	}
	GDScriptParser parser;
	if (OK != parser.parse(source, p_path, false)) {
		return;
	}
	for (const String &E : parser.get_dependencies()) {
		p_dependencies->push_back(E);
	}
}
Error ResourceFormatSaverGDScript::save(const Ref<Resource> &p_resource, const String &p_path, uint32_t p_flags) {