Here's how I think of it using the teleportation by destruction method.
CryptoPrime steps into the teleportation pad. he gets scanned, then destroyed.
CryptoClone steps out of the other teleportation pad, but remembers stepping in as Prime.
Prime is dead, but only Prime knows that he's dead. Clone may be told that Prime is dead, but as Clone's identity is Prime, he would be unable to believe being told that "he" is dead.