### 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
_find_and_save_edited_subresources(scene, processed, flags);
	for (int i = 0; i < scene->get_child_count(); i++) {
		Node *n = scene->get_child(i);
		if (n->get_owner() != editor_data.get_edited_scene_root()) {
			continue;
		}
		_save_edited_subresources(n, processed, flags);
	}
}
void EditorNode::_find_node_types(Node *p_node, int &count_2d, int &count_3d) {
	if (p_node->is_class("Viewport") || (p_node != editor_data.get_edited_scene_root() && p_node->get_owner() != editor_data.get_edited_scene_root())) {
		return;
	}
	if (p_node->is_class("CanvasItem")) {
		count_2d++;
	} else if (p_node->is_class("Node3D")) {
		count_3d++;
	}
	for (int i = 0; i < p_node->get_child_count(); i++) {
		_find_node_types(p_node->get_child(i), count_2d, count_3d);
	}
}
void EditorNode::_save_scene_with_preview(String p_file, int p_idx) {