### 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
disk_changed_list->clear();
	TreeItem *r = disk_changed_list->create_item();
	disk_changed_list->set_hide_root(true);
	bool need_reload = false;
	
	for (int i = 0; i < editor_data.get_edited_scene_count(); i++) {
		Ref<DirAccess> da = DirAccess::create(DirAccess::ACCESS_RESOURCES);
		if (editor_data.get_scene_path(i) == "" || !da->file_exists(editor_data.get_scene_path(i))) {
			continue;
		}
		uint64_t last_date = editor_data.get_scene_modified_time(i);
		uint64_t date = FileAccess::get_modified_time(editor_data.get_scene_path(i));
		if (date > last_date) {
			TreeItem *ti = disk_changed_list->create_item(r);
			ti->set_text(0, editor_data.get_scene_path(i).get_file());
			need_reload = true;
		}
	}
	String project_settings_path = ProjectSettings::get_singleton()->get_resource_path().path_join("project.godot");
	if (FileAccess::get_modified_time(project_settings_path) > ProjectSettings::get_singleton()->get_last_saved_time()) {
		TreeItem *ti = disk_changed_list->create_item(r);
		ti->set_text(0, "project.godot");
		need_reload = true;
	}
	if (need_reload) {
		disk_changed->call_deferred(SNAME("popup_centered_ratio"), 0.3);
	}
}
void EditorNode::_resave_scenes(String p_str) {