A Bank Draft is legally not the same as a cheque, therefore whereas banks can try and watch out for it, legally placing a stop on it is very difficult. When they issued you a replacement draft, normal practise would be that whatever they asked you to sign contained an indemnity in which you guaranteed to pay the replacement if it surfaced, albeit they should have credited your account back with the value of the first one. In other words, they should have credited your account with the value of the first draft, but if it was ever paid, they'd be within their rights to debit your account.
From what you are saying, they don't ever seem to have credited your account back. They should be able to check to see if the original draft was ever cashed, if it wasn't they should credit your account back. However, if it was cashed, you are at a probable loss. They may be able to tell you where it was lodged to and you could try and get the funds back from them, but if the original draft was stolen for example, I'd say you would have very little chance