### 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
Node *edited_scene_root = editor_data.get_edited_scene_root(i);
			if (edited_scene_root) {
				List<Node *> valid_nodes;
				find_all_instances_inheriting_path_in_node(edited_scene_root, edited_scene_root, p_instance_path, valid_nodes);
				if (valid_nodes.size() > 0) {
					edited_scene_map[i] = valid_nodes;
				}
			}
		}
	}
	if (edited_scene_map.size() > 0) {
		
		Error err;
		Ref<PackedScene> instance_scene_packed_scene = ResourceLoader::load(p_instance_path, "", ResourceFormatLoader::CACHE_MODE_IGNORE, &err);
		instance_scene_packed_scene->set_path(p_instance_path, true);
		ERR_FAIL_COND(err != OK);
		ERR_FAIL_COND(instance_scene_packed_scene.is_null());
		HashMap<String, Ref<PackedScene>> local_scene_cache;
		local_scene_cache[p_instance_path] = instance_scene_packed_scene;
		for (const KeyValue<int, List<Node *>> &edited_scene_map_elem : edited_scene_map) {
			
			int current_scene_idx = edited_scene_map_elem.key;
			editor_data.set_edited_scene(current_scene_idx);
			Node *current_edited_scene = editor_data.get_edited_scene_root(current_scene_idx);
			
			EditorUndoRedoManager::get_singleton()->clear_history();
			
			editor_data.is_scene_changed(current_scene_idx);
			for (Node *original_node : edited_scene_map_elem.value) {