Error with Sunrise.php and issues with loading subfolder sites

After making some updates I am receiving a has an invalid domain setting in the multi-network I am running.

I have 4 networks setup in the multi-site and 3 of the networks are functioning properly.

The 3rd network - subfolder domains are now redirecting and giving 404 errors on the root site. The root site has also lost it's graphic links.

I am unable to remove or change the domain mapping for the network.

I am also getting an error with sunrise php that gives me the notice "move the line define( 'SUNRISE', 'on' ); above the last require_once() in that file or make sure you updated sunrise.php."

I am on nginx.