A user can only be truly deleted from the WorkflowGen database if they are not referenced anywhere in WorkflowGen. If they are referenced, then the user will be archived. Archiving means that the username will be renamed and will be set to archived status, and the user will no longer be able to access the application.
A user is archived when:
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You have manually deleted the user in the Administration Module/Directory/Users and the user has done something in WorkflowGen (you can see the details via the Activity Report link in the User form).
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The directory synchronization process has deleted a user who has done something in WorkflowGen.