Wait, the John from the new Alpha Timeline (Alpha-Prime, maybe?) died when LOWAS exploded, and the old Alpha John, with old Alpha Roxy, took his place in Alpha-Prime. But what about Roxy Prime? We haven't seen her die. Are there two Roxys now?

Roxy Prime was killed by Heiress Jane when she jumped in front of Rose and took a forky thing to the body. It was heroic, many tears were shed.