Update Commerce Kickstart

Updating your files
If you are upgrading your site from a previous release of Commerce Kickstart (since 2.x RC1 forward), we support an upgrade path.

IMPORTANT - Drush 8.x-6.x supports an upgrade for Kickstart 2, but it is not the common "drush up" command. Use the following code snippets (and make sure to backup everything):

$ drush dl commerce_kickstart $ drush updatedb -y
Or you can follow the step by step instructions below.

Log in to your site as admin (user 1)
Create a complete backup of your files and database. (This can be accomplished with Backup & Migrate or Drush)
Download the latest release of Kickstart 2 by scrolling down to the bottom of the page and choosing between a tar.gz and a .zip file.
NOTE You absolutely want to download the full package with core, as Kickstart 2 does ship with core patches
Extract to an empty folder
Delete all files and folders on your site except the sites folder (remember you should have a backup before doing this)
Copy or Move all files and folders except the sites/ folder from the new release to your current site.
Go to /update.php and run any and all updates.
Be happy because you are now on the latest release of all that is fantastic with Kickstart 2