I'm reading this differently...

I simply want to remove one copy of the pair

This would indicate that pairs somehow got reversed and duplicated.
So duplicate pairs needs to be removed, resulting in 2 equal length arrays.

use strict;
my @dataA = qw(1 9 3 5 4 2);
my @dataB = qw(3 2 1 6 7 9);

my $i = 0;
foreach my $num (@dataA) {
    foreach (@dataB) {
        if ($num == $_) {
            splice(@dataA,$i,1);
            splice(@dataB,$i,1);
        }
    }
    $i++;
}
print "@dataA\n@dataB\n";
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