Plugins not activated/don’t contain information when migrating

Hello! I am following along with the staging to production migration tutorial. I have manually overwritten the wp-content/uploads, wp-content/plugins and wp-content/themes folders from the staging site to the live site. I then run the search and replace according to the tutorial.

After this process has completed, the live site DOES have the plugins from the staging site, but they are not activated and do not contain any saved data. None of my updated designs are on the live site. In addition, on the staging site I had made changes to the navigation, and I do not see those changes reflected on the live site. Could you please help me?