Mark the domain as deleted by running the commadmin domain delete command. (See the Chapter 5, Command Line Utilities, in Sun Java System Communications Services 6 2005Q4 Delegated Administrator Guide).
Remove services from the users of that domain.
A service can be a mailbox or a calendar. For Messaging Server, the program is called msuserpurge. (See msuserpurge in Sun Java System Messaging Server 6 2005Q4 Administration Reference. For calendar services, the program is csclean. (See Sun Java System Calendar Server Administration Guide.)
Permanently remove the domain, by invoking the commadmin domain purge command.