Last time I did something like this, I grabbed the .torrent file from the completed archive, told it to start downloading it again. It recreated the folder structure and names it expected, then I stopped it, and put the completed files back where it was expecting to see them with the names that it had just created. I started it again to let everything force check. Then I use the torrent client to move the files to where I wanted them.
I've honestly given up one having my torrent* client put the files in their ultimate locations. I just have it make copies of the completed files and leave the torrents the hell alone.
*edit: dictation shenanigans