One more reason to like all new versions of uTorrent

Stats are saved in the tracker not in your client. At every 30mins the client send information to the server with your uploaded and downloaded bytes, so your client may have different stats from the server, it doesn't matter even if you reset your client stats.
Just download the torrent files again and force recheck/rehash (uTorrent does it automatically if you don't remove skip hash recheck option). Are you sure that you lost even a single file (they can be in the download folder, but just not in the program)? It is hard to lose a file under NTFS after all.