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It is in fact as easy as this:
Start / Run -> cmd: dsmgmt metadata cleanup metadata cleanup: connections server connections: connect to server server.domain.local q metadata cleanup: select operation target select operation target: list domains select operation target: select domain (%d of unwanted Domain) select operation target: list naming contexts select operation target: select naming context (%d of naming conext to remove) q metadata cleanup: remove selected naming context (repeat selecting naming contexts for all specified)