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I have deleted a user from AD, i want their user profile and mysite removed. I understand that is the role of the My Site Clean Up timer job. Although it seems the bdeleted field is never changed to 1. When i manually change bdeleted=1 and manually run the My Site Clean Up timer job it works and the user profile and mysite is removed.

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After deleting the user from AD, have you started a full sync in User profile service application?

If not, you need to run a full sync via user profile service application->start profile synchronization, then check again.

Reference: SharePoint: The complete guide to user profile cleanup – Part 3 – 2013

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