Don’t use bench drop-site if you don’t want to delete the site.
If only removing domain name you can use bench setup remove-domain (see bench setup --help)
Once you have done this, regenerate the nginx configurations, restart nginx and reload nginx: bench setup nginx sudo service nginx restart sudo service nginx reload
Remove site from disk and database completely
bench drop-site [domain-name] --root-user --root-password
Above i stated more in detail. but choice would be yours.