Warning: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list.d/backports.list:1 and /etc/apt/sources.list.d/freedombox2.list:4
Also 11 others “configured multiple times” in the same two places.
/etc/apt/sources.list.d/backports.list:1
and
/etc/apt/sources.list.d/freedombox2.list:4
I know how to fix it but I don’t know which version should be kept, backports or freedombox?
Yes, keep the entry in freedombox2.list and get rid of the one that is in backports.list. That file is used by FreedomBox to update and manage packages, so the system will work right once the duplicates are gone. After that, use "sudo apt update" to double-check that there are no more warnings.