Here's my go:

It's written in long hand with lots of variables to help (me) 'see' the method.

It loads the updates into a hash then loops through the data one line at a time making changes when the id matches and writing everything to a new file.

Any use?

#!/bin/perl5

use strict;
use warnings;

my %update;
open (UPDATE, "update.txt") or die "Cannot open update.txt";
while (<UPDATE>){
  chomp;
  # T00001    0123-12345    DD001    67
  my @array = split '\t';
  my $key = $array[0];
  $update{$key} = [ @array[1..3] ]
}
close (UPDATE);

open (MDF, 'mdfl.txt') or die "Cannot open update.txt";
open (OUT, '>', 'out.txt')  or die "Cannot open out.txt";

while (<MDF>){
  chomp;
  my $record = $_;
  my @fields = split '\t', $record;
  my $dmpiid = $fields[0];
  if ( exists $update{$dmpiid} ){
    my $curr = $fields[4];
    my $update = $update{$dmpiid}[2];
    $fields[3] = $curr;
    $fields[4] = $update;
    $record = join "\t", @fields;
  }
  print OUT $record, "\n";
}    

close (MDF);
close (OUT);
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