You said:

my $keys = {};
while (<FILEHANDLE>) {chomp; $keys[$_] = 1;}
[download]

$keys is not an array, you've defined it as a hash reference. You meant $keys->{$_} ....

Then you said:

exists($keys, $recordArray[2])
[download]

exists() does not work like that.

exists $keys->{$recordArray[2]};
[download]

Please, if you don't test the code you supply, acknowledge that in writing.