According to Cryptum, the "real" Didact was killed. However, the brevet mutation that the Didact performed on Bornstellar passed on all of his memories to Bornstellar. It was a dillema that Bornstellar had been facing since the mutation but he wasn't sure exactly what was happening to him. At the end of Cryptum, Bornstellar realized that the memories he was having were actually the Didact's. When Bornstellar approached the Librarian, he embraced her saying something along the lines of "My wife, I've missed you". In a sense, he had become the Didact only in Bornstellar's body. As for Bornstellar and the Librarian, i guess we will find out what happens to them in Primordium.