It isn't necessary to do all of the intermediate processing. You can read a line and check it all at the same time.

The line is used as a hash key. The value is tested before being incremented and the line is added to the array.

my %seen;
while (<PROCESSED_FILE>){
    push @unique, $_ unless $seen{$_}++;
}
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This is OK if the hash doesn't grow to big. Using MD5 hashes of lines is an uesful technique.