You don't need a while-loop. You should use a for-loop.
And the test if any element is in the array should be unless(@array){...}.
You have to use the modifier g to delete "all" things from '#' to the end of line...

#!/usr/bin/perl

use strict;
use warnings;

{
  local $/;
  open DATA, '<',"san.txt" or die $!;

  my @blocks = map { [ split /\n/ ] }
       ( split /(?=ITEM NO:)/, ( map { s/#.*?\n//sg; $_ } <DATA> )[0] 
+);
  close DATA;

  for(@blocks){
    my @array = @$_; 
    unless(@array){
      print "There is no item remaining in the file";
      last;
    }
    print "@array\n"; 
  }
}
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