If you're having this problem with BitTornado:
It's a known bug. Close BT, push Ctrl+Alt+Del, then pick the "Processes" tab (Win XP only), then find "btdownloadgui". Highlight it, and click "End Process". Now open the torrent back up, point it to the folder to which you were downloading it before, and start it back up again. BT should then scan the existing data that you already downloaded, and pick up where it left off.
If you're having this problem with another client, I don't know what to tell you. You can try this method, but I can't guarantee that it will totally solve your problem.
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