This is a broad question, but as far as I know, the only two ways to delete a course is:
GUI with system admin privileges > select course dropdown > delete
GUI > delete courses by DSK
In other words, the SIS advanced field settings do not allow you to delete courses, only disable them. I know you self-hosted folks can delete courses directly through the database, but this question is for Managed Hosting folks.
Big question: have you seen any other scenario where a course has been deleted? Another question, how did you track down which system administrator performed the delete?
Minor edit for clarity Message was edited by: Christin Deville