You can goto the URL opera://about, take note of the "profile" path, close Opera and edit the "Preferences" file in the profile folder with JSONedit in tree mode. Under root, if you see "protocol_handler", you can right-click "protocol_handler" and choose "delete selected node" and save your changes. That should reset the magnet protocol settings for Opera. Or, you can look under root/protocol_handler/allowed_origin_protocol_pairs and make sure "magnet" is set to true for each site listed there. Or, you can delete the node for each site you don't want so that you get asked again by Opera on those sites.
If you open up a command prompt and run:
start "Magnet test" "magnet://test", does qBittorrent start up?