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When deleting rows from a table in the base state (state 0), the compress operation may inadvertently not delete the object's corresponding geometry in the feature and spatial index tables. The issue is specific to tables registered as versioned and stored as SDEBINARY.
When the compress operation is deleting rows from a versioned class' base table (state 0), there are specific conditions when the row's geometry in the feature table and spatial index table are also not deleted.
The orphaned rows in the feature and spatial index table do not cause or lead to any problems. The rows are completely orphaned and consuming storage space in the tables.
To remove the additional rows requires the feature class to be unregistered as versioned.
The owner of the feature class can either use the Unregister as versioned command in ArcCatalog or the sdetable -o alter_reg command.