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my %seen;

...
   print($fh_out1 $_) if $seen{$_} > 0;
   print($fh_out2 $_) if $seen{$_} < 0;
}

my %seen1; ++$seen1{$_} while <$fh_in1>;
my %seen2; ++$seen2{$_} while <$fh_in2>;

print $fh_out1 grep !$seen2{$_}, keys %seen1;
print $fh_out2 grep !$seen1{$_}, keys %seen2;