### 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
if (PE->get().type == Variant::OBJECT && value.is_zero() && !(PE->get().usage & PROPERTY_USAGE_STORE_IF_NULL)) {
					continue;
				}
				String vars;
				VariantWriter::write_to_string(value, vars, _write_resources, this);
				f->store_string(name.property_name_encode() + " = " + vars + "\n");
			}
		}
		if (E->next()) {
			f->store_line(String());
		}
	}
	if (packed_scene.is_valid()) {
		
		Ref<SceneState> state = packed_scene->get_state();
		for (int i = 0; i < state->get_node_count(); i++) {
			StringName type = state->get_node_type(i);
			StringName name = state->get_node_name(i);
			int index = state->get_node_index(i);
			NodePath path = state->get_node_path(i, true);
			NodePath owner = state->get_node_owner_path(i);
			Ref<PackedScene> instance = state->get_node_instance(i);
			String instance_placeholder = state->get_node_instance_placeholder(i);
			Vector<StringName> groups = state->get_node_groups(i);
			Vector<String> deferred_node_paths = state->get_node_deferred_nodepath_properties(i);
			String header = "[node";
			header += " name=\"" + String(name).c_escape() + "\"";
			if (type != StringName()) {
				header += " type=\"" + String(type) + "\"";
			}