### 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
continue;
								}
								const GDScriptParser::ClassNode *inner_class = subclass->members[i].m_class;
								if (inner_class->identifier->name == extend_classes[0]->name) {
									extend_classes.remove_at(0);
									found = true;
									subclass = inner_class;
									break;
								}
							}
							if (!found) {
								subclass = nullptr;
								break;
							}
						}
					}
				} else if (subclass->extends.size() == 1) {
					*r_base_type = subclass->extends[0]->name;
					subclass = nullptr;
				} else {
					break;
				}
			} else {
				*r_base_type = "RefCounted";
				subclass = nullptr;
			}
		}
	}
	if (r_icon_path) {
		*r_icon_path = c->simplified_icon_path;