DocumentStatus 16 within the [ControlPointMetaStore].[Metadata].[Document] table is for files that have been disposed via ControlPoint policy. Once an Incremental scan is executed, the connector will identify that the files no longer exist in the source repository and send Delete actions to MetaStore which will remove those documents from the [ControlPointMetaStore].[Metadata].[Document] table. What you are seeing is expected behaviour as we don't keep references of deleted files in the Document table once re-scanned.
If you have any further issues on this please raise a support ticket and I will be happy to assist.