my %values_by_id;

# for each line from the first file:
my($id1, $values_string1) = split /:/, $line1;
for my $value1 (split /~~/, $values_string1) {
  # set each unique value to be true in the hash
  $values_by_id{$id1}{$value1} = 1;
}

# and then for a line from the second file:
my($id2, $values_string2) = split /:/, $line2;
my @shared_values;
for my $value2 (split /~~/, $values_string2) {
  push @shared_values, $value2 if $values_by_id{$id2}{$values2};
}