One possible way would be to do a routine that calculates the next state from the previous one no matter how many 'N's are in the array. That way you just put the number of 'N's at the beginning of the array and call the routine repeatedly until all 'N's are at the end of the array

use warnings;
use strict;
my @arr=qw/A B C D E F/;

my $anzahl=2;

unshift @arr, ('N') x $anzahl;

print join (",",@arr),"\n";

while (@arr= step (@arr)) {
  print join (",",@arr),"\n";
}


sub step {
# returns empty list if all marks are already at the end
  my @arr= @_;
  my $marksatend=0;
  my $i= @arr;
  #count marks at the end
  while ($i) {
    if ($arr[--$i] eq 'N') {
      $marksatend++;
    }
    else {
      last;
    }
  }
  #find a mark to advance
  my $mark=-1;
  while ($i) {
    if ($arr[--$i] eq 'N') {
      $mark=$i;
      last;
    }
  }
  #advance
  if ($mark<0) {
      return ();
  }
  else {
    my $tmp= $arr[$mark];
    $arr[$mark]= $arr[$mark+1];
    $arr[$mark+1]= $tmp;
    if ($marksatend>0) {
      splice @arr,-$marksatend;
      splice @arr,$mark+2,0, ('N')x$marksatend;
    }
    return @arr;
  } 
}
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