### 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
error = OK;
					if (cache_mode != ResourceFormatLoader::CACHE_MODE_IGNORE) {
						if (!ResourceCache::has(res_path)) {
							resource->set_path(res_path);
						}
						resource->set_as_translation_remapped(translation_remapped);
					}
				}
				return error;
			}
			if (!assign.is_empty()) {
				bool set_valid = true;
				if (value.get_type() == Variant::OBJECT && missing_resource != nullptr) {
					
					
					
					Ref<MissingResource> mr = value;
					if (mr.is_valid()) {
						missing_resource_properties[assign] = mr;
						set_valid = false;
					}
				}
				if (value.get_type() == Variant::ARRAY) {
					Array set_array = value;
					bool is_get_valid = false;
					Variant get_value = resource->get(assign, &is_get_valid);
					if (is_get_valid && get_value.get_type() == Variant::ARRAY) {
						Array get_array = get_value;
						if (!set_array.is_same_typed(get_array)) {
							value = Array(set_array, get_array.get_typed_builtin(), get_array.get_typed_class_name(), get_array.get_typed_script());