I don't get why people are shocked that Kronika is back. She couldn't kill Raiden because he was an elder god, and since she's a titan she is not able to be killed. Liu Kang clearly got cocky thinking he had the game figured out, but Kronika is a master at this shyt.
Kronika clearly was killed though in both the Liu Kang and Shang Tsung ending. Liu Kang didn't erase the villains, he altered their destinies according to Geras in the Keepers of Time trailer.
What we're seeing in the exchange between Kronika and Shang Tsung is an altered version of their original destinies. Kronika is no longer Keeper of Time obviously because Liu Kang is.