When you download the latest version of Pipeline, the new theme will be added to the drafts section of your store and is completely separate from your live theme that's running your store.
Your current live theme is not affected by downloading the latest version of Pipeline.
The new theme is in draft mode which allows you to setup and configure, while your store continues to operate with the current theme.
Helpful article by Shopify on updating themes:
Shopify Help Center
Steps for updating your theme
Create a backup of your existing theme. This will be used to copy settings and to keep the live theme running without interruption.
Visit the Shopify Theme Store and log in. For paid themes, it is important to log in to the account that you used to buy the theme. This will prevent you from being asked to buy the theme again. Direct link for the Theme Store for Story: