SharePoint User Profile Import and My Site Deletion

What Profile Import does when a user account Deleted in AD?
When a user account deleted/disabled in Active directory (or any other account store where SharePoint gets the profiles) SharePoint profile import makes the missing profile as “Marked for deletion” in the Profile database.

In fact, Profile import makes the profiles in the profile database as “Marked for deletion” based on User Profile filters applied. (If you change the filter, it will take effect on the next profile import). By default it will be:

(&(objectCategory=Person)(objectClass=User))
 Which instruct profile import: only get the user objects

You can make it:
(&(objectCategory=person)(objectClass=user)( !(userAccountControl:1.2.840.113556.1.4.803:=2)))
Which instruct profile import: only get the user objects and omit disabled ones.

Refer to my post: Filters in SharePoint User Profile Synchronization Connections for other supported user profile filters.

My Site Cleanup Job:
The timer Job “My Site Cleanup Job” Which Runs hourly, looks for all users marked for deletion during profile import (Incremental or Full which doesn’t matters) and deletes their profiles from the profile database. It also assigned ownership to the deleted profile’s manager(if available) and an email is sent to the manager.

When the My site cleanup job deletes the user profile, it also deletes all profile-specific data including any user Quick Links, Colleague Tracker, Profile Picture, etc. (But the user’s documents in My site will be in safe)

When My site will be deleted?
Although it sounds like “My Site Cleanup Job” it doesn’t actually delete my sites. It only removes the user profile from the profile store and changes my site owner to the user’s manager if there is one.  My Site will only be deleted if the Automatic Site Deletion is enabled. If you want to enforce the Automatic deletion of my sites you can use “Site Use Confirmation and Deletion”
(Central Administration > Application Management > Site Use Confirmation and Deletion)

If a user profile is missing during profile import, and if you try to get into My Site’s URL by:  https://mysite.company.com/personal/person.aspx?accountname=domain\user – SharePoint will display “user not found” error message.

which is obvious! Change the secondary owner if you want to access the user’s My site.

As the user is not found, You can’t change the secondary owner from central Admin web interface. Use stsadm: E.g.
stsadm -o siteowner -url https://mysite.company.com/personal/E372488 -secondarylogin global\salaudeen”

More info:
https://blogs.technet.com/b/seanearp/archive/2009/03/04/sharepoint-profile-cleanup.aspx
https://www.sharepointjoel.com/Lists/Posts/Post.aspx?ID=532
https://technet.microsoft.com/en-us/library/ff681014.aspx