Leo says that it's too risky and not really worth it to dive into trying to get rid of duplicate data. Hard drives are so cheap and large, that it's better to just get another hard drive. Just consider the duplicates as another backup! There is a good search tool called X1 that can search his backups. Variety with backup is a good thing.
The chatroom says he can keep a catalog on his computer that has a database of what he has in offline storage. There are a few apps for this: