Here's a suggestion, just to make sure you are looking at the right evidence when you say that the append operation is not working on the file (I'm also fixing your indentation a bit, and improving the error checking/reporting):

my $original_size = -s $target_full_path;  # how many bytes in the fil
+e

open( my $out, ">>", $target_full_path)    # I like using lexical file
+ handles, and
    or die "Can't open $target_full_path: $!"; # reporting system erro
+r messages

while($fetchdata=$sth4->fetchrow_array()) 
{ 
    print $fetchdata;
    print $out $fetchdata or die "print to file failed: $!";
    $rowcount++;
}
close $out or die "Unable to close output file: $!"; 
print $rowcount;

my $current_size = -s $target_full_path;  # how many bytes now

printf( "File %s was %d bytes, is now %d bytes\n",
      $target_full_path, $original_size, $current_size );
[download]

Maybe the reports you get from that version will tell you what you need to know.