Actually it doesn't matter where the torrent file is stored (I always download to my desktop for ease of deleting after I start).
You don't even need to delete the old torrent. The important thing is to download the newly uploaded torrent and start seeding with that and keep seeding.
With uTorrent there is yet another copy of the new torrent stored in the uTorrent folder which is the working copy.
I don't know with qBittorrent but suspect it will be similar.