### 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
} break;
					case GDScriptParser::ClassNode::Member::SIGNAL: {
						_signals[member.signal->identifier->name] = member.signal->method_info;
					} break;
					case GDScriptParser::ClassNode::Member::GROUP: {
						members_cache.push_back(member.annotation->export_info);
					} break;
					default:
						break; 
				}
			}
		} else {
			placeholder_fallback_enabled = true;
			return false;
		}
	} else if (placeholder_fallback_enabled) {
		return false;
	}
	placeholder_fallback_enabled = false;
	if (base_cache.is_valid() && base_cache->is_valid()) {
		for (int i = 0; i < base_caches.size(); i++) {
			if (base_caches[i] == base_cache.ptr()) {
				if (r_err) {
					*r_err = true;
				}
				valid = false; 
				base_cache->valid = false;
				base_cache->inheriters_cache.clear(); 
				base_cache.unref();
				base.unref();