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Hi KSMB_2020,
Thanks for posting in the community. We are happy to help you.
Based on my testing, the "Profiles Missing from Import" view (the MarkDeleted view) will list all deleted users, including the user whose OneDrive site is in the retention period, the user whose OneDrive site has exceeded the retention period but is still in the built-in OneDrive deletion process, and users in other situations.
That's because in addition to the retention policy, Microsoft also provides the built-in OneDrive deletion process. When a user is deleted, his OneDrive site will still remain for 93 days (the default is 93 days but can be changed by the tenant admin). For more explanation, you can view Point 3 and Point 4 in this article: The OneDrive deletion process.
For users in other situations, I'm referring to tenant administrators manually forcing the deletion of a user's OneDrive site after deleting the user's account. This will also cause that user to appear in the list (in the "Profiles Missing from Import" view). At this point, if you click on “Manage Personal Site”, the opened page will return a 404 error message.
Regarding your concern "Some sites have the data, some are empty".
Since the tenant administrator can give another user access to the deleted user's OneDrive, the manager can back up or move the deleted user's OneDrive file to another location during the OneDrive deletion process. For those empty sites, I believe that the relevant manager has moved these files from those sites to another location, therefore those sites are empty.
Since Microsoft 365 retention settings from retention policies and retention labels always take precedence to the standard OneDrive deletion process, regarding your question, it should be 365 days (your retention value) + 93 days (the default). After that, these OneDrive sites will be automatically permanently deleted and cannot be recovered.
When you have any updates or concerns, please feel free and come back to share them with us. We are willing to help you. 😊
Sincerely,
George | Microsoft Community Moderator