Eu tive o mesmo problema depois de ativar a arquitetura externa para o arm:
dpkg --print-foreign-architectures
i386
armvfp
armhf
Isso impediu que apt update
fosse totalmente concluído. Sempre terminava com:
N: Skipping acquire of configured file 'main/binary-armhf/Packages' as repository 'http://apt.llvm.org/xenial llvm-toolchain-xenial-3.9 InRelease' doesn't support architecture 'armhf'
N: Skipping acquire of configured file 'main/binary-armhf/Packages' as repository 'http://apt.llvm.org/xenial llvm-toolchain-xenial InRelease' doesn't support architecture 'armhf'
N: Skipping acquire of configured file 'non-free/binary-armhf/Packages' as repository 'http://repository.spotify.com stable InRelease' doesn't support architecture 'armhf'
W: http://ppa.launchpad.net/colingille/freshlight/ubuntu/dists/vivid/Release.gpg: Signature by key 3764AB961B292804CD3474FAEAE2E8E7CB7F5C71 uses weak digest algorithm (SHA1)
E: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/xenial/main/binary-armhf/Packages 404 Not Found [IP: 91.189.91.23 80]
E: Failed to fetch http://security.ubuntu.com/ubuntu/dists/xenial-security/main/binary-armhf/Packages 404 Not Found [IP: 91.189.91.26 80]
E: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/xenial-proposed/main/binary-armhf/Packages 404 Not Found [IP: 91.189.91.23 80]
E: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/xenial-updates/main/binary-armhf/Packages 404 Not Found [IP: 91.189.91.23 80]
E: Some index files failed to download. They have been ignored, or old ones used instead.
Enquanto os erros eram apenas para arm, impedia a instalação de muitos pacotes. A remoção dessas arquiteturas com sudo dpkg --remove-architecture armvfp
e sudo dpkg --remove-architecture armhf
seguido por apt update
resolveu os problemas.
Eu sei que a pergunta do OP já foi respondida, mas os mesmos sintomas ocorreram no meu caso.