Used Space is not updated correctly on System Health screen after manual cleanup.
Archive Shuttle updates the “Used Space” value for specific links on the System Health screen from related Item (Link) database with the SQL query below.

SELECT ISNULL(SUM(ExportedSizeOriginal - ImportedSizeOriginal), 0)
       FROM ItemRoutingStatistics WITH (NOEXPAND)
           WHERE ExportedSizeOriginal > ImportedSizeOriginal

Used space is updated whenever items are exported or imported and the item database is updated, also when a mapping which is not completely synced is removed.
Archive Shuttle does not update the “Used Space” when there are failed items which stay on the staging area or when mappings are manually removed from it.
To know which items are cleaned up from staging area read this KB article.

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