### 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 (implicit_initializer) {
		clear_data->functions.insert(implicit_initializer);
		implicit_initializer = nullptr;
	}
	if (implicit_ready) {
		clear_data->functions.insert(implicit_ready);
		implicit_ready = nullptr;
	}
	if (static_initializer) {
		clear_data->functions.insert(static_initializer);
		static_initializer = nullptr;
	}
	_save_orphaned_subclasses(clear_data);
#ifdef TOOLS_ENABLED
	
	if (_owner) {
		_clear_doc();
	}
#endif
	
	if (is_root) {
		
		for (GDScriptFunction *E : clear_data->functions) {
			memdelete(E);
		}
		for (Ref<Script> &E : clear_data->scripts) {
			Ref<GDScript> gdscr = E;
			if (gdscr.is_valid()) {
				GDScriptCache::remove_script(gdscr->get_path());
			}