### 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 (reloading) {
		return OK;
	}
	reloading = true;
	bool has_instances;
	{
		MutexLock lock(GDScriptLanguage::singleton->mutex);
		has_instances = instances.size();
	}
	ERR_FAIL_COND_V(!p_keep_state && has_instances, ERR_ALREADY_IN_USE);
	String basedir = path;
	if (basedir.is_empty()) {
		basedir = get_path();
	}
	if (!basedir.is_empty()) {
		basedir = basedir.get_base_dir();
	}
	
#ifdef TOOLS_ENABLED
	if (EditorPaths::get_singleton() && basedir.begins_with(EditorPaths::get_singleton()->get_project_script_templates_dir())) {
		reloading = false;