$re = '/(?:\G(?!^)|\[)[^][,]*\K,(?=[^][]*])/m';
$str = '"Hello", "Goodbye", ["Yes", "No", "Maybe], "Indeed", ["Why", "What"]';
$subst = ";";
$result = preg_replace($re, $subst, $str);
echo "The result of the substitution is ".$result;
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php