### 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 (!dummy_read.resource_map.has(id)) {
					Ref<DummyResource> dr;
					dr.instantiate();
					dr->set_scene_unique_id(id);
					dummy_read.resource_map[id] = dr;
					uint32_t im_size = dummy_read.resource_index_map.size();
					dummy_read.resource_index_map.insert(dr, im_size);
				}
			} else {
				type = res_type;
				String uid_text = ResourceUID::get_singleton()->id_to_text(res_uid);
				id = type + "_" + uid_text.replace("uid://", "").replace("<invalid>", "0");
				main_res = true;
			}
			local_offsets.push_back(wf2->get_position());
			bs_save_unicode_string(wf, "local://" + id);
			local_pointers_pos.push_back(wf->get_position());
			wf->store_64(0); 
			bs_save_unicode_string(wf2, type);
			uint64_t propcount_ofs = wf2->get_position();
			wf2->store_32(0);
			int prop_count = 0;
			while (true) {
				String assign;
				Variant value;
				error = VariantParser::parse_tag_assign_eof(&stream, lines, error_text, next_tag, assign, value, &rp_new);
				if (error) {
					if (main_res && error == ERR_FILE_EOF) {
						next_tag.name = ""; 
						break;