### 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
CharString utf8 = p_string.utf8();
	if (p_bit_on_len) {
		p_f->store_32((utf8.length() + 1) | 0x80000000);
	} else {
		p_f->store_32(utf8.length() + 1);
	}
	p_f->store_buffer((const uint8_t *)utf8.get_data(), utf8.length() + 1);
}
Error ResourceLoaderText::save_as_binary(const String &p_path) {
	if (error) {
		return error;
	}
	Ref<FileAccess> wf = FileAccess::open(p_path, FileAccess::WRITE);
	if (wf.is_null()) {
		return ERR_CANT_OPEN;
	}
	
	static const uint8_t header[4] = { 'R', 'S', 'R', 'C' };
	wf->store_buffer(header, 4);
	wf->store_32(0); 
	wf->store_32(0); 
	wf->store_32(VERSION_MAJOR);
	wf->store_32(VERSION_MINOR);
	static const int save_format_version = BINARY_FORMAT_VERSION;
	wf->store_32(save_format_version);
	bs_save_unicode_string(wf, is_scene ? "PackedScene" : resource_type);
	wf->store_64(0); 
	wf->store_32(ResourceFormatSaverBinaryInstance::FORMAT_FLAG_NAMED_SCENE_IDS | ResourceFormatSaverBinaryInstance::FORMAT_FLAG_UIDS);