This solution was given to us by the Ensim staff, as a paid support request. Hopefully, if you’re reading this, you will not have to buy a support ticket:

To delete the sites manually you will have to do the following:1. Find the siteID.sitelookup -d domainname2.cd /etc/virtualhosting/mappings/grep siteID *3. Remove the entry from domainmap file and regenerate the domainmap.db usingmakemap hash domainmap.db < domainmap4. cd /home/virtual/rm -rf siteID/5. Remove any apache entries.cd /etc/httpd/conf/rm -rf siteID siteID.previewcd virtualrm -f siteIDcd ../virtual.previewrm -f siteID6. Restart httpd.service httpd restart7. Remove cron jobscd /etc/cron.weekly/rm -f 0virtualhosting.siteIDcd ../cron.daily/rm -f 0virtualhosting.siteID