### 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
ERR_FAIL_COND(!instantiated_node);
				bool original_node_is_displayed_folded = original_node->is_displayed_folded();
				bool original_node_scene_instance_load_placeholder = original_node->get_scene_instance_load_placeholder();
				
				instantiated_node->set_name(original_node->get_name());
				
				String original_node_file_path = original_node->get_scene_file_path();
				if (current_edited_scene == original_node) {
					instantiated_node->set_scene_instance_state(original_node->get_scene_instance_state());
					
					if (original_node_file_path.is_empty()) {
						Ref<SceneState> state = current_packed_scene->get_state();
						state->set_path(current_packed_scene->get_path());
						instantiated_node->set_scene_inherited_state(state);
						instantiated_node->set_scene_file_path(String());
					}
					editor_data.set_edited_scene_root(instantiated_node);
					current_edited_scene = instantiated_node;
					if (original_node->is_inside_tree()) {
						SceneTreeDock::get_singleton()->set_edited_scene(current_edited_scene);
						original_node->get_tree()->set_edited_scene_root(instantiated_node);
					}
				}
				
				original_node->replace_by(instantiated_node, false);
				
				original_node->queue_free();
				
				instantiated_node->set_display_folded(original_node_is_displayed_folded);
				instantiated_node->set_scene_instance_load_placeholder(original_node_scene_instance_load_placeholder);