The strings in the  @w array seem to have whitespace before the first single-quote. Any leading whitespace will remain after the single-quotes are deleted from the string. Is this whitespace expected? Use of
    print Dumper \@w;
would make any leading (or trailing) whitespace obvious.

BTW: All single-quotes could be deleted from a string in a single
    $w[0]=~s/'//g;
statement. Please see perlre, perlretut and perlrequick, and Regexp Quote-Like Operators in perlop for s///g. All single-quotes could be deleted from every string in an array with
    s/'//g for @w;
(but this still leaves any whitespace untouched).

Ah, the joys of debuging by proxy. it seems i missed something in the debug statements and print 'new  cu1:'.$cu1."\n"; should have been print 'cui1    :'.$cui1."\n"; and print 'new  cu2:'.$cu2."\n"; should have been print 'cui2    :'.$cui2."\n";

but this simple exercise has located the problem anyway, in that on i=405 the cu1/cu2 arrays are empty. that means the pops return undef and hence your error. is there anything different about 405? as noted by AnomalousMonk the strings in @w have leading spaces, is that true only on 405? Maybe that is the problem and needs to be fixed somehow, in @new or by regexp maybe.

to workaround this for now you could change to

      unless (scalar(@{$cu1})) {print "cu1 is empty\n"; next} 
      my $cui1 =pop @{$cu1};

      ########################################
      print 'cui1    :'.$cui1."\n"; 
      ########################################

      my $cu2 = $umls->getConceptList($t2);***error

      ########################################
      print 'raw  cu2:'.$cu2."\n"; 
      print 'size cu2:'.scalar(@{$cu2})."\n"; 
      print 'cu2     :'.join('|',@{$cu2})."\n"; 
      ########################################

      unless (scalar(@{$cu2})) {print "cu2 is empty\n"; next} 
      my $cui2 = pop @{$cu2};

      ########################################
      print 'cui2    :'.$cui2."\n"; 
      ########################################
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