In your loop on @rawdata you match on $string, which is undefined. If you replace it with $value, your code works for me.

It might be worth considering to use use strict; and use warnings;, because these point out some errors.

I would also replace the first if with

if($value =~ /# __START_CONFIG__/i) {
  $action=2;
  print outfile1 $value;
  next;
}
[download]

to ensure that this line ends up in the first file. I didn't encounter problems re-running the script, so I can't help you on that one.