### 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
p_ownership_table.insert(p_current_node, p_current_node->get_owner());
	for (int i = 0; i < p_current_node->get_child_count(); i++) {
		Node *child = p_current_node->get_child(i);
		update_ownership_table_for_addition_node_ancestors(child, p_ownership_table);
	}
}
void EditorNode::update_diff_data_for_node(
		Node *p_edited_scene,
		Node *p_root,
		Node *p_node,
		HashMap<NodePath, ModificationNodeEntry> &p_modification_table,
		List<AdditiveNodeEntry> &p_addition_list) {
	bool node_part_of_subscene = p_node != p_edited_scene &&
			p_edited_scene->get_scene_inherited_state().is_valid() &&
			p_edited_scene->get_scene_inherited_state()->find_node_by_path(p_edited_scene->get_path_to(p_node)) >= 0;
	
	Node *valid_node_owner = p_node->get_owner();
	while (valid_node_owner) {
		if (valid_node_owner == p_root) {
			break;
		}
		valid_node_owner = valid_node_owner->get_owner();
	}
	if ((valid_node_owner == p_root && (p_root != p_edited_scene || !p_edited_scene->get_scene_file_path().is_empty())) || node_part_of_subscene || p_node == p_root) {