While working for a project of SharePoint 2010 we came across the issue of reflection of users in MySite organisation Chart even though the users are removed from the Active Directory.
Below are the tasks we performed for troubleshooting the issue,.
1. Went through User Profile service application and verified profile in missing profiles list.
2. Run full crawl for search service application.
3. Navigated to monitoring–> Check the status of my site cleaner job —> made it enable.
4. Then executed the my site cleaner job.