### 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
res->set_edited(false);
	}
	for (const String &E : edited_resources) {
		Ref<Resource> res = ResourceCache::get_ref(E);
		if (!res.is_valid()) {
			continue; 
		}
		Ref<PackedScene> ps = res;
		if (ps.is_valid()) {
			continue; 
		}
		ResourceSaver::save(res, res->get_path(), flg);
		saved++;
	}
	EditorUndoRedoManager::get_singleton()->set_history_as_saved(EditorUndoRedoManager::GLOBAL_HISTORY);
	return saved;
}
static void _reset_animation_players(Node *p_node, List<Ref<AnimatedValuesBackup>> *r_anim_backups) {
	for (int i = 0; i < p_node->get_child_count(); i++) {
		AnimationPlayer *player = Object::cast_to<AnimationPlayer>(p_node->get_child(i));
		if (player && player->is_reset_on_save_enabled() && player->can_apply_reset()) {
			Ref<AnimatedValuesBackup> old_values = player->apply_reset();
			if (old_values.is_valid()) {
				r_anim_backups->push_back(old_values);
			}
		}
		_reset_animation_players(p_node->get_child(i), r_anim_backups);
	}
}
void EditorNode::_save_scene(String p_file, int idx) {