All the sites managed the visual upgrade except the top level site. You can run this Powershell script to upgrade all sites in a site collection:
$site = Get-SPSite(“https://webappurl“)
foreach ($web in $site.AllWebs) { $web.UIVersion = 4; $web.Update() }
After running this, the top level site was in preview mode with a link in a yellow bar giving the option to upgrade the site. Click on the yellow bar and it will take you to the following page:
https://webappurl/_layouts/prjsetng.aspx
In the Visual Upgrade options, select “
note:
I think you could probably do this at a top level site by going to https://webappurl/_layouts/prjsetng.aspx and selecting upgrade interface and then the buttons would be ungrayed. Best practice to do a visual upgrade in powershell and loop through all the sites in a site collection.