### 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
if (p_res.is_null()) {
		return false;
	}
	if (processed.has(p_res)) {
		return processed[p_res];
	}
	bool changed = p_res->is_edited();
	p_res->set_edited(false);
	bool subchanged = _find_and_save_edited_subresources(p_res.ptr(), processed, flags);
	if (p_res->get_path().is_resource_file()) {
		if (changed || subchanged) {
			ResourceSaver::save(p_res, p_res->get_path(), flags);
		}
		processed[p_res] = false; 
		return false;
	} else {
		processed[p_res] = changed;
		return changed;
	}
}
bool EditorNode::_find_and_save_edited_subresources(Object *obj, HashMap<Ref<Resource>, bool> &processed, int32_t flags) {