my @new_order = (0, 1, 2, 3, 5, 4);

my @AoA = (
  [
      qw(1 2 3 4 5 6),
  ],
  [
      qw(a b c d e f),
  ],
);

my @new_aoa;

for (@AoA){
    push @new_aoa, [@$_[@new_order]];
}

print Dumper \@new_aoa;