Different output than wanted.

$find = '.5010.';

$dirname = '79';
if(!is_dir($dirname))
    mkdir($dirname, 0777);

$directory_with_files = './';
$dh  = opendir($directory_with_files);
$files = array();
while (false !== ($filename = readdir($dh)))
{
    if(in_array($filename, array('.', '..')) || is_dir($filename))
        continue;

    $files[] = $filename;
}


foreach($files as $file)
{
    //find only 5010 files
    if(stripos($file, $find) !== false)
    {
        // open the 5010 file
        $handle = fopen($file, "r");
        $file_content = file_get_contents($file);
     
        
        if ($handle) {
            $header = '';
            $name = '';
            $footer = '';
            $payor_blocks = array();
            
            
            // determine if file has more than one payor
            $payor_count = substr_count($file_content, 'N1*');
            //if the file has more than one payor
            if($payor_count > 1) {
                //read the file line by line
                $header_end = false;
                $block_start = false;
                $count = 1;

                
                while (($line = fgets($handle)) !== false) {
                    //look for the first payor block
                    if(strpos($line, 'N1*') !== false || $block_start) {
                        $header_end = true; $block_start = true;
                        //see if the block finished
                        if(strpos($line, 'CAS~') !== false) {
                            $block_start = false;
                            $payor_blocks[$count] .= $line;
                            $count++;
                        }
                        $payor_blocks[$count] .= $line;
                    } else {
                        //append to the header
                        if($header_end) {
                            $footer .= $line."\n";
                        } else {
                            $header .= $line."\n";
                        }
                    }
                }

                //get payor blocks and create a file foreach payor
                $new_files = array();
                foreach($payor_blocks as $block) {
                    $filename = $file . "_" . $count;
                    $count++;
                    $new_files[] = array(
                        'name' => $filename,
                        'content' => $header."\n".$block."\n".$footer	
                    	
                    );
                    
//footer prints out after the first CAS and all the rest
                }
                echo "<pre>" . print_r($new_files, true) . "</pre>";
                //loop through new files and create them
                foreach($new_files as $new_file) {
                    //create file
                	$myfile = fopen($file, "w");
      	
                	fwrite($myfile, $new_file['content']);	
              		//close the file
                	fclose($myfile);
                }
                
            } else {

            	// DO what u were doing in script #1
           while (($line = fgets($handle)) !== false)
            {
            	$refid = 'REF';
            	
            	if(stripos($line, $refid) !== false)
            	{
            		$refnumber = str_replace(array($refid, '~'), array('', ''), $line);
            		$refnumber = trim($refnumber);
            	
            		if($refnumber != '')
            		{
            			$refnumber = '_'.$refnumber.'_';
            			$filerenamed = str_replace($find, $refnumber, $file);
            			copy($file, $dirname.'/'.$filerenamed);
            		}
            		echo $refnumber . "\n";
            	}
            	}
            	 
            }
        }
        // DONE - close the file
        fclose($handle);
    }
}

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