Chrome was opening my magnet files with Stremio which didn't work at all. So I wanted to convince it to open them with my torrent client qBittorent. What I did is that I edited:
/home/denijane/.config/mimeapps.list
adding the line:
x-scheme-handler/magnet=org.qbittorrent.qBittorrent.desktop
I saved it and restarted Chrome and voila!
Useful konsole commands:
xdg-mime query default x-scheme-handler/magnet
and
gio mime x-scheme-handler/magnet
and also the .desktop files seem to reside in /usr/share/applications/
Also you can try to update the database with "update-desktop-database" but in my case it didn't seem to work, but closing and opening Chrome did.