I had a case where a deleted user was not in the CWP MySQL DB, but still left a trailing CentOS user and config files.
sudo userdel -f $USER
to delete the user account, home directory, and mail spool.
But then I had to do a locate $USER
to find other straggler files (SSL, MySQL DB backups, Apache logs, etc.). Then I manually deleted all those orphaned files. Then I could re-migrate the user from a cPanel server.