Maybe Archer was always a cyborg?
Think about it. How many times has he been stabbed and shot and he never dies? Maybe he did die one of those times and was replaced with one of Krieger's models. Although how did he father a baby (unless he was replaced after that or Krieger figured out some kind of cyborg sperm system!)?
Maybe that is a cyborg dead in the swimming pool and the real Archer is in cold storage, ready to be thawed out and cured by Krieger?
But if indeed that is the real Archer floating there and he is replaced by a cyborg, that will change the entire show, and perhaps not for the better. I don't know. So many directions this show can take.