From the sounds of it, you have two AoAs like the following:

my @array1 = (
   [ id1, ... 169 other fields ... ],
   [ id2, ... 169 other fields ... ],
   ... ~200k other records ...
);

my @array2 = (
   [ id2, ... 169 other fields ... ],
   [ id5, ... 169 other fields ... ],
   ... ~50k other records ...
);
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Start by making it easy to find records in array2.

my %array2 = map { $_->[0] => $_ } @array2;
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Then the problem becomes trivial.

for my $array1_rec (@array1) {
   my $array2_rec = $array2{ $array1_rec->[0] }
      or next;

   ... Change @$array1_rec based on values from @$array2_rec ...
}
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You don't actually need to create @array1 or @array2.