### Godot version

v4.1.dev.custom_build [a8453cb33]

### System information

Windows 11, Core i5-12400F, RX 6600

### Issue description

in recent custom 4.1 builds it is regening every ext id on every save even if just one simple file

	[gd_scene load_steps=2 format=3 uid="uid://bj3w1run711x7"]

	[ext_resource type="Texture2D" uid="uid://c082xolc76p8n" path="res://icon.svg" id="1_ftki2"]

	[node name="Node2D" type="Node2D"]

	[node name="Sprite2D" type="Sprite2D" parent="."]
	position = Vector2(351, 294)
	texture = ExtResource("1_ftki2")

can use a script like this save all files and regen all ext ids in project

	@tool
	extends EditorScript

	func listFiles(path: String, extensions: Array = []) -> Array:
		var list := []
		for dir in DirAccess.get_directories_at(path):
			if not dir.begins_with("."):
				list.append_array(listFiles(path + dir + "/", extensions))
		for file in DirAccess.get_files_at(path):
			var ext := file.split(".")[-1]
			if not file.begins_with(".") and ext != "import":
				if extensions.is_empty() or ext in extensions:
					list.append(path + file)
		return list

	func _run() -> void:
		for file in listFiles("res://", ["tscn", "tres"]):
			ResourceSaver.save(load(file))

in 4.0.2 this script does not regen every ext id in the project each time it is run (just when needed) but in latest 4.1 it does
but just ctrl+s works'nt too

thanks

thought it was related to this but maybe not
https://github.com/godotengine/godot/issues/76693

### Steps to reproduce

- make new scene with ext resource (new control, new sprite, set texture to icon)
1 - save, stage changes
2 - goto 1

or can use script on any project to see that it applies to everything, everywhere, all at once


### Minimal reproduction project

n/a
}
	
	_find_resources(p_resource, true);
	if (packed_scene.is_valid()) {
		
		for (int i = 0; i < packed_scene->get_state()->get_node_count(); i++) {
			if (packed_scene->get_state()->is_node_instance_placeholder(i)) {
				continue;
			}
			Ref<PackedScene> instance = packed_scene->get_state()->get_node_instance(i);
			if (instance.is_valid() && !external_resources.has(instance)) {
				int index = external_resources.size() + 1;
				external_resources[instance] = itos(index) + "_" + Resource::generate_scene_unique_id(); 
			}
		}
	}
	{
		String title = packed_scene.is_valid() ? "[gd_scene " : "[gd_resource ";
		if (packed_scene.is_null()) {
			title += "type=\"" + _resource_get_class(p_resource) + "\" ";
			Ref<Script> script = p_resource->get_script();
			if (script.is_valid() && script->get_global_name()) {
				title += "script_class=\"" + String(script->get_global_name()) + "\" ";
			}
		}
		int load_steps = saved_resources.size() + external_resources.size();
		if (load_steps > 1) {
			title += "load_steps=" + itos(load_steps) + " ";
		}
		title += "format=" + itos(FORMAT_VERSION) + "";