Site Not Updating After Saving - Multisite/Pro Sites

I have created a new "SITE" in my Multisite network. I am working on designing the site so it can be replicated for a new "Blog Templates" theme.

I am trying to update the site with a new logo or other items. When I upload the logo it will be visible in the "Media" section but will not actually update on the live site.

Anyone know what I am missing and why the new site will not hold the updates?