VigilEnt Security Manager 4.0
Only the linked user account(s) get deleted when selecting a Master Account and specifying 'Delete User'.
This is by design. In the VigilEnt Security Operations Console (VSOC), selecting the Master User Account and specifying VSM Actions | Delete User will only affect the linked user accounts. When taking this action, a dialog box comes up indicating 'This action will be taken against all linked users.'
To remove a Master Account within VSOC, select the Master Account, right-click the account and select VSM Actions | Unlink Synched User from the context menu.