Is your feature request related to a problem? Please describe.
If the apt-file package is installed, apt update requests the Contents-$arch metadata file. When it isn't found, apt cannot update from that repo.
Describe the solution you'd like
The solution would be to sync the Contents-$arch metadata files.
Describe alternatives you've considered
Because apt fails when apt-file is installed, the only alternative is to purge apt-file and do filelist lookups againts packages.ubuntu.com or packages.debian.org.