$re = '/\.zip\b[^,]*(*SKIP)(*F)|\s/m';
$str = 'http://abcd.com/old file/anotherfile.zip/some contents/sample.txt,http://abcd.com/new file/anotherfile.zip/some more contents/new sample.txt,http://abcd.com/newer file/another file.zip/some more contents/old sample.txt,http://abcd.com/newer file/another file.txt
';
$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