.htaccess www. redirect in Dev Desktop
Yes, you need to use a separate .htaccess file for your local version of the site.

It often makes sense to sync just the sites/all and/or sites/default folders (minus settings.php of course) of a Drupal site, so you can avoid this sort of problem without even having to think about it; unless you're hacking at core of course, which isn't recommended anyway :)