### 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
case Variant::ARRAY: {
				Array varray = obj->get(E.name);
				int len = varray.size();
				for (int i = 0; i < len; i++) {
					const Variant &v = varray.get(i);
					Ref<Resource> res = v;
					if (_find_and_save_resource(res, processed, flags)) {
						ret_changed = true;
					}
				}
			} break;
			case Variant::DICTIONARY: {
				Dictionary d = obj->get(E.name);
				List<Variant> keys;
				d.get_key_list(&keys);
				for (const Variant &F : keys) {
					Variant v = d[F];
					Ref<Resource> res = v;
					if (_find_and_save_resource(res, processed, flags)) {
						ret_changed = true;
					}
				}
			} break;
			default: {
			}
		}
	}
	return ret_changed;
}
void EditorNode::_save_edited_subresources(Node *scene, HashMap<Ref<Resource>, bool> &processed, int32_t flags) {