You want to check if you've seen the key (not the line), so the key is what you should be putting into the hash. For some definition of extract_key,

my @unique = grep { my $key = extract_key($_);
                    ! $seen{ $key }++
                  }
             @newFile;
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In this case,

my @unique = grep !$seen{ substr($_, 9, 5) }++, @newFile;
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