If you want to remove a Secondary Domain, open its Domain Settings page, and click the Remove Domain button. The confirmation page appears. If the Empty Domains Only option is selected, a Secondary Domain is removed only if there are no Accounts in it. Otherwise, all Domain Accounts are permanently removed, too.
If you confirm the action, the selected Domain, its settings, all its Accounts and other Objects will be permanently removed.
You cannot remove a Domain when any of its Accounts is in use.