Answer by cadesalaberry for Chrome doesn't open automatically magnet links anymore

There are two protocol_handler keys in the Preferences json object.

{  ..."profile": {"avatar_bubble_tutorial_shown": 2,"avatar_index": 26,"blacklisted_credentials_normalized": true,"content_settings": {      ..."ppapi_broker": {},"protocol_handler": {},"sensors": {},      ...    },"protocol_handler": {"excluded_schemes": {"magnet": false    }  },  ...}

Make sure to modifiy the one at the root. If you modify the one in the profile, it will be renamed to protocol_handler,* and considered invalid.