### Godot version

3.5.2.stable, 4.0.1.stable

### System information

Arch Linux

### Issue description

When the `Show Hidden Files` property is enabled in the Editor Settings:
![image](https://user-images.githubusercontent.com/6501975/226908540-8e70e520-3dcd-46e4-beaf-103ac176c1de.png)
Any `FileDialog` nodes from the project will inherit this setting, and their `Show Hidden Files` property is set to true everytime the scene is re-opened:

https://user-images.githubusercontent.com/6501975/226909135-a8fafdf7-ca36-40aa-b69a-a7baf2d7ae4f.mp4


This occurs on 3.5.2 as well.

### Steps to reproduce

- Enable `Show Hidden Files` property in the Editor Settings:
    - Reload Godot for the bug to occur
- Create a FileDialog node, and set it's `Show Hidden Files` property to false
- Save and close the scene, and reopen it
- The `Show Hidden Files` property is reset to true.

### Minimal reproduction project

N/A
immediate_dialog_confirmed = true;
}
bool EditorNode::immediate_confirmation_dialog(const String &p_text, const String &p_ok_text, const String &p_cancel_text) {
	ConfirmationDialog *cd = memnew(ConfirmationDialog);
	cd->set_text(p_text);
	cd->set_ok_button_text(p_ok_text);
	cd->set_cancel_button_text(p_cancel_text);
	cd->connect("confirmed", callable_mp(singleton, &EditorNode::_immediate_dialog_confirmed));
	singleton->gui_base->add_child(cd);
	cd->popup_centered();
	while (true) {
		OS::get_singleton()->delay_usec(1);
		DisplayServer::get_singleton()->process_events();
		Main::iteration();
		if (singleton->immediate_dialog_confirmed || !cd->is_visible()) {
			break;
		}
	}
	memdelete(cd);
	return singleton->immediate_dialog_confirmed;
}
void EditorNode::cleanup() {
	_init_callbacks.clear();
}
int EditorNode::get_current_tab() {