The data migration is done via APIs to create data (BAPIs and function modules). It is not possible to delete migrated data via the Migration Cockpit. If the given application to maintain a business object (e.g. Business partner like Customer, Supplier) is able to delete existing business objects, the migrated data might be deleted using this app. For some business data there are Mass Maintaince apps available that may support the deleting of existing data. But this depends on the application. For some transactional data it migth also be possible to do a reverse posting via such maintenance apps. For example, knowing the document number of the inverntory balance you can cancel that document.
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