### 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 (d.has("hint_string")) {
						pinfo.hint_string = d["hint_string"];
					}
					if (d.has("usage")) {
						pinfo.usage = d["usage"];
					}
					if (d.has("class_name")) {
						pinfo.class_name = d["class_name"];
					}
					ERR_CONTINUE(pinfo.name.is_empty() && (pinfo.usage & PROPERTY_USAGE_STORAGE));
					ERR_CONTINUE(pinfo.type < 0 || pinfo.type >= Variant::VARIANT_MAX);
					props.push_back(pinfo);
				}
			}
		}
		
		Vector<_GDScriptMemberSort> msort;
		for (const KeyValue<StringName, GDScript::MemberInfo> &F : sptr->member_indices) {
			if (!sptr->members.has(F.key)) {
				continue; 
			}
			_GDScriptMemberSort ms;
			ms.index = F.value.index;
			ms.name = F.key;
			msort.push_back(ms);
		}
		msort.sort();
		msort.reverse();
		for (int i = 0; i < msort.size(); i++) {
			props.push_front(sptr->member_indices[msort[i].name].property_info);