To check this assumption I have added an extra row of data "2 2 9 2 2". That row cannot match any of the other rows and therefore should not be deleted.

use Modern::Perl qw/2015/;

my %data;

# First we transform and load the data into a hash
while (<DATA>) {
    chomp;
    my $data = $_;
    s/([^9 ])/[$1X]/g;
    s/9/[0129]/g;
    s/X/9/g;
    $data{$_} = $data;
}

#Then we check if records with missing data are unique
for my $testrecord ( keys %data ) {
    next unless $data{$testrecord} =~ m/9/;
    for my $record ( keys %data ) {
        next if $data{$record} eq $data{$testrecord}; #don't check you
+rself
        if ( $data{$record} =~ m/$testrecord/ ) {
            delete $data{$testrecord};
            last;
        }
    }
}
say $data{$_} for keys %data;

__DATA__
2 2 0 1 0
2 2 0 2 1
0 2 1 1 0
0 1 1 1 0
2 2 0 0 0
2 9 0 2 1
0 2 0 1 0
2 2 0 9 0
2 2 9 2 2
[download]

0 1 1 1 0
0 2 0 1 0
2 2 0 1 0
2 2 0 0 0
2 2 0 2 1
0 2 1 1 0
2 2 9 2 2
[download]