Must run twice for it to work fully

$find = '.5010.';
$directory_with_files = './'.date('m-d-Y');
$dh  = opendir($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
        $handle = fopen(date('m-d-Y').'/'.$file, "r");
        $file_content = file_get_contents(date('m-d-Y').'/'.$file);
        $handle2 = fopen(date('m-d-Y').'/'.$file, "r");
        $file_content2 = file_get_contents(date('m-d-Y').'/'.$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;

                
           if($handle2){
                $line_number = 0;
                $line_stop= array();
                while (($line1 = fgets($handle2)) !== false) {
                
                	$line_number++;
                
                	if(strpos($line1, 'CAT') !==false){
                		 
                		$line_stop[] = $line_number;
                	}
                
                }
                $footer_line = count($line_stop)-2;
                $footer_line = $line_stop[$footer_line];
                
                
                $line_number = 0; }
                
                //look for occurances of CAT and what line each on is on
               
                while (($line = fgets($handle)) !== false) {
                    $line_number++;
                   

                    //look for the first payor block
                    if(strpos($line, 'N1') !== false || $block_start) {
                        $header_end = true; $block_start = true;
                         if(strpos($line, 'N1') !== false) {
                         	$count++;
                         }  
                            
                        //see if the block finished
                         if($line_number == $footer_line) {
                         	$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) {
                    $filename = date('m-d-Y').'/'.$file . "_" . $count;
                    $count++;
                    $new_files[] = array(
                        'name' => $filename,
                        'content' => $header."\n".$block."\n".$footer	
                    	
                    );
                 
                }
                //loop through new files and create them
                foreach($new_files as $new_file) {
                    //create file
                	$myfile = fopen($new_file['name'], "w");
   
                    //put contents in the file               	
                	fwrite($myfile, $new_file['content']);	
              		//close the file
                	fclose($myfile);
                }
                
             echo "<pre>" . print_r($new_files, true) . "</pre>";
            } 
            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('./'.date('m-d-Y').'/'.$file, './'.date('m-d-Y').'/'. $filerenamed);
            		}
            		echo $refnumber . "\n";
            		
            	}
            
            	}
            }
        }

    }
    		// DONE - close the file
    			fclose($handle);
}

foreach($files as $fiftyfile){
	if(stripos($fiftyfile, $find) !== false){

		$handle3 = fopen(date('m-d-Y').'/'.$fiftyfile, "r");
		$file_content3 = file_get_contents(date('m-d-Y').'/'.$fiftyfile);

		if ($handle3) {

			if(unlink('./'.date('m-d-Y').'/'.$fiftyfile))
			{
				echo "file named $fiftyfile has been deleted successfully";
			}
			else
			{
				echo "file is not deleted";
		}
}
}

}
		//combine all files
		file_put_contents("combined.txt", ""); // Empty the file first
		foreach ($files as $my_file) {
		$handle4 = fopen(date('m-d-Y').'/'.$my_file, "r");
		$file_content4 = file_get_contents(date('m-d-Y').'/'.$my_file);
		file_put_contents("combined.txt", $file_content4, FILE_APPEND);

}