"Special Processes" should be audited regardless of the level of control that exists. Those controls and the methods / procedures are typically a complex set of interactions that need to be rigorously followed and in environments where they are manually conducted have a multitude of opportunities for errors to occur. Auditing of "Special Processes" that are automated may not require the same frequency of audit as a manually run process, but they should not be exempt from the audit process either. There are several other threads with similar themes, particularly Heat Treating, under which you can find some further information & possibly a checklist or two.