What has likely happened is that an anti-piracy company detected the file at the time you were downloading it (much like a speed camera while speeding) and sent a complaint to your ISP. Even though you were no longer sharing the file, your ISP is not the one who detected this, so when they received the letter, this led them to believe that you are still sharing it even though your are not and thus took action.
Basically, what you need to do is tell your ISP that you have deleted this and your Internet connection should be restored. Your ISP will not check if you're still sharing it. However, that anti-piracy organisation may still be watching your IP address (or the IP address you had at the time if it's dynamic), so you will need to extra careful when using BitTorrent or file sharing software.
I would also suggest running PeerBlock (freeware utility) on your PC anytime you use file sharing software. While this will not make it safe to illegally download films, music, etc., it will at least significantly reduce the number of anti-piracy organisation hosts spying on your transfers and also reduce the likelihood of false positives and connecting to bandwidth wasters.