UPDATE: Sorry I think I messed up here. Is this something like you want? My brain is hurting today. 
use strict;
use warnings;

while (<DATA>)
{
   next unless /\S/;
   chomp;
   my ($name, $markerA, $markerB, $height)
       = split (/\s+/,$_);
   $name    //= "";
   $markerA //= ""; $markerA ="" if $markerA =~ /^0$/;
   $markerB //= ""; $markerB ="" if $markerB =~ /^0$/;
   if ($markerA !~ /A/)
   {
      $markerA = $markerB;
      $markerB = "B";
   }
   
   $height  //= "";
   
   if (!$height)
   {
      my $string;
      foreach ($name, $markerA, $markerB)
      {
         $string .= "\'$_\',";
      }
      chop $string;
      print "$string\n"; 
   }      
}     
=prints
'2','A',''
'3','','B'
=cut


#Name Marker1 Marker2 Height Time
__DATA__
1 A A 6246 0.9706

1 B B 3237 0.9706

2 A 0

2 B B 5495 0.9775

3 A A 11254 0.9694

3 B 0

[download]
I think this could be done better. Below was a admittedly failed bogus solution for first post. 
use strict;
use warnings;

my %name;
while(my $line =<DATA>)
{
    next unless $line =~ /\S/; #skip blank lines
    chomp $line;
    my ($undef, $markerName,undef,
        undef, $height) = split (/\s+/, $line);         
    $name{$markerName} = $height;    
}

foreach (sort keys %name)
{
   print "$_ => $name{$_}\n";
}  

=prints
a => 55
b => 32
c => 34
=cut


__DATA__
1 a 23 99999 55
4 c 55 8888 34

5 b 45 88888 32

[download]

In reply to Re: Combine duplicated keys in Hash array by Marshall
in thread Combine duplicated keys in Hash array by Tikplay

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