$re = '/(?:\baccord\b|\G(?<!^))[^)\s]*\K\s+/m';
$str = 'A scripture reference like [Luke 2:12, 16](accord://read/?Luke 2:12, 16) should be clickable.';
$subst = "%20";
$result = preg_replace($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