Hi, I think you have to ssh into your Homestead box, go to the nginx directory, and then delete the files for the old apps from the sites-enabled and sites-available directories. Here's an example:
Go to sites-enabled directory
cd /etc/nginx/sites-enabled
Run ls to see all files
ls
Remove the file corresponding to the old site, replacing my-site.app with the name of the file.
sudo rm my-site.app
Do the same above, for the file(s) in the /etc/nginx/sites-available directory, then restart the nginx server with:
sudo service nginx restart
Also, don't forget to delete the site's definition from your Homestead.yaml file.
Hope that helps.