### 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
GDScriptInstance *instance = memnew(GDScriptInstance);
	instance->base_ref_counted = p_is_ref_counted;
	instance->members.resize(member_indices.size());
	instance->script = Ref<GDScript>(this);
	instance->owner = p_owner;
	instance->owner_id = p_owner->get_instance_id();
#ifdef DEBUG_ENABLED
	
	for (const KeyValue<StringName, MemberInfo> &E : member_indices) {
		instance->member_indices_cache[E.key] = E.value.index;
	}
#endif
	instance->owner->set_script_instance(instance);
	
	{
		MutexLock lock(GDScriptLanguage::singleton->mutex);
		instances.insert(instance->owner);
	}
	_super_implicit_constructor(this, instance, r_error);
	if (r_error.error != Callable::CallError::CALL_OK) {
		instance->script = Ref<GDScript>();
		instance->owner->set_script_instance(nullptr);
		{
			MutexLock lock(GDScriptLanguage::singleton->mutex);
			instances.erase(p_owner);