I noticed when deleting the accounts they are removed from SiteWorx Secondary List and the main (symbolic link based folders e.g. /home/account/mysecondarydomain.com/html) are removed.
But the actual data storage folders (e.g. /home/account/mainaccount.com/html/mysecondarydomain.com) still have all the data.
Seems like those are just kind of orphaned.
Looks like this has to do with cPanel imports and not really the secondary account setup in the main system