I am now seeing that message about multiple times so can see why you cleared all the files, not sure why message still showing though
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list.d/sonarr.list:1 and /etc/apt/sources.list.d/sonarr.list:3
W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list.d/sonarr.list:1 and /etc/apt/sources.list.d/sonarr.list:3
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/sonarr.list:1 and /etc/apt/sources.list.d/sonarr.list:3
W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list.d/sonarr.list:1 and /etc/apt/sources.list.d/sonarr.list:3