chomp(my @checked_names = do {
    open my $fh, "<", $config_file ? (<$fh>) :
    $! =~ /no such file/i          ? ()      :
        die "Can't open $config_file to read: $!";
});

# ... do stuff with @checked_names

open my $fh, ">", $config_file or die "Can't open $config_file to write: $!";
print $fh map "$_\n", @checked_names;
close $fh;