### 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
int flg = 0;
	if (EDITOR_GET("filesystem/on_save/compress_binary_resources")) {
		flg |= ResourceSaver::FLAG_COMPRESS;
	}
	flg |= ResourceSaver::FLAG_REPLACE_SUBRESOURCE_PATHS;
	HashSet<String> edited_resources;
	int saved = 0;
	List<Ref<Resource>> cached;
	ResourceCache::get_cached_resources(&cached);
	for (Ref<Resource> res : cached) {
		if (!res->is_edited()) {
			continue;
		}
		String path = res->get_path();
		if (path.begins_with("res:")) {
			int subres_pos = path.find("::");
			if (subres_pos == -1) {
				
				edited_resources.insert(path);
			} else {
				edited_resources.insert(path.substr(0, subres_pos));
			}
		}