When the Delete File toggle is ON, the system now removes the last Cloud Document, which is not associated with any Salesforce record (except self-user) during Real-Time migration.
PS: View Drag, Drop & Upload Files to Amazon S3, a Salesforce AppExchange app for moving files from Salesforce to Amazon S3: https://appexchange.salesforce.com/appxListingDetail?listingId=a0N3000000B5ZPqEAN