### 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 (clearing) {
		return;
	}
	clearing = true;
	ClearData data;
	ClearData *clear_data = p_clear_data;
	bool is_root = false;
	
	
	if (clear_data == nullptr) {
		clear_data = &data;
		is_root = true;
	}
	{
		MutexLock outer_lock(func_ptrs_to_update_mutex);
		for (UpdatableFuncPtr *updatable : func_ptrs_to_update) {
			bool destroy = false;
			{
				MutexLock inner_lock(updatable->mutex);
				if (updatable->transferred) {
					func_ptrs_to_update_main_thread.mutex.lock();
				}
				for (GDScriptFunction **func_ptr_ptr : updatable->ptrs) {
					*func_ptr_ptr = nullptr;
				}
				DEV_ASSERT(updatable->rc != 0);
				updatable->rc--;
				if (updatable->rc == 0) {
					destroy = true;