Once an user object has been migrated over into the Strategy Enterprise Manager Warehouse (using the data load process), if it gets deleted in the project Metadata, it will not get deleted from the Strategy Enterprise Manager Warehouse.
To filter out user objects in Strategy Enterprise Manager that no longer exist in the project Metadata, the Configuration Object Exists Status indicator must be used.
For more information on how to update the Configuration Object Exists Status indicator, please review the following Technical Note:
KB37196: How to update the "Configuration Object Exists Status" indicator in MicroStrategy Enterprise Manager 9.x?
Once the Configuration Object Exists Status indicator has been updated user can build a simple report using the User attribute and the Configuration Object Exists Status indicator to filter out users that no longer exists in the Project Metadata:

The report showed above is a simple Enterprise Manager report built based in the Strategy Tutorial Project. Note that users that have been deleted from the Strategy Tutorial Project has the Configuration Object Exists Status ID = '0' and its description as ALREADY DELETED FROM THE MD REPOSITORY.
Using the Configuration Object Exists Status indicator, Enterprise Manager administrators can filter out users that no longer exist in the project Metadata from the Enterprise Manager reports.