### 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
if (err != OK) {
		show_accept(TTR("Couldn't save scene. Likely dependencies (instances or inheritance) couldn't be satisfied."), TTR("OK"));
		return;
	}
	int flg = 0;
	if (EDITOR_GET("filesystem/on_save/compress_binary_resources")) {
		flg |= ResourceSaver::FLAG_COMPRESS;
	}
	flg |= ResourceSaver::FLAG_REPLACE_SUBRESOURCE_PATHS;
	err = ResourceSaver::save(sdata, p_file, flg);
	
	emit_signal(SNAME("scene_saved"), p_file);
	_save_external_resources();
	editor_data.save_editor_external_data();
	for (Ref<AnimatedValuesBackup> &E : anim_backups) {
		E->restore();
	}
	if (err == OK) {
		scene->set_scene_file_path(ProjectSettings::get_singleton()->localize_path(p_file));
		editor_data.set_scene_as_saved(idx);
		editor_data.set_scene_modified_time(idx, FileAccess::get_modified_time(p_file));
		editor_folding.save_scene_folding(scene, p_file);
		_update_title();
		_update_scene_tabs();
	} else {
		_dialog_display_save_error(p_file, err);
	}
	scene->propagate_notification(NOTIFICATION_EDITOR_POST_SAVE);
}
void EditorNode::save_all_scenes() {