My output has a "?" on the name and the file doesn't open anymore

<?php // demo/temp_jasmine.php
/**
 * https://www.experts-exchange.com/questions/28966264/My-output-has-a-on-the-name-and-the-file-doesn't-open-anymore.html
 *
 For example; My file is 4867586.5010.476564.ed
 After the code executes and reads the file, the output should be: 4867586_SMIL01_476564.ed but instead its: 4867586_SMIL01
 And when I checked it out on putty the file name was: 4867586_SMIL01?_476564.ed
 */
error_reporting(E_ALL);

//expression to be found in file name
$find = '.5010.';

//directory name
//we will store renamed files here
$dirname = '5010';
if(!is_dir($dirname)) mkdir($dirname, 0777);

//read all files from a directory
//skip directories
$directory_with_files = './';
$directory_with_files = 'storage'; // USE THIS DIRECTORY FOR TESTS

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

    $files[] = $filename;
}

//iterate collected files
foreach($files as $file)
{
    //check if file name is matching $find
    if(stripos($file, $find) !== false)
    {
        $handle = fopen($directory_with_files . DIRECTORY_SEPARATOR . $file, "r");
        if ($handle)
        {
            while (($line = fgets($handle)) !== false)
            {
                $line = trim($line); // REMOVE UNWANTED WHITESPACE CHARACTERS
                //find REF line
                $refid = 'REF*2U*';
                if(stripos($line, $refid) !== false)
                {
                    $refnumber = str_replace(array($refid, '~'), array('', ''), $line);
                    $refnumber = trim($refnumber); // REMOVE UNWANTED WHITESPACE CHARACTERS
                    var_dump($refnumber);
                    if($refnumber != '')
                    {
                        $refnumber = '_'. $refnumber .'_';
                        $filerenamed = str_replace($find, $refnumber, $file);
                        copy($directory_with_files . DIRECTORY_SEPARATOR . $file, $dirname . DIRECTORY_SEPARATOR . $filerenamed);
                    }
                    echo $refnumber . "\n";
                } // END IF
            } // END WHILE READING FILE
            fclose($handle);
        }
    } // END IF FILENAME MATCH
}

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<?php
error_reporting(E_ALL);

// Some setup stuff
$find = '.5010.';
$dirname = 't1517/5010';

// Get list of files using glob with wildcard
$files = glob("t1517/*{$find}*");

//iterate collected files
foreach($files as $file) {
  // Read all the lines in the file into an array
  $lines = file($file);
  
  // Iterate over the array of lines
  foreach($lines as $line) {
   
    // check if line contains search string
    // using preg_match to check and extract 
    // reference at the same time
    if (preg_match("/REF\*2U\*(.*?)\~/", $line, $match)) {
    
    // glob uses full paths so extract the filename from
    // the path
      $newfile = basename(str_replace($find, "_{$match[1]}_", $file));
    
    // Some debug code
      echo "f: {$file}, NF: {$newfile}<br/>";
    
    // And finally do the copy.
      copy($file, "{$dirname}/{$newfile}");
    }
  }
}

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... potential to grow ...