Well we all wanted to know "What If", meaning what if somehow they got their memories back. What then? Well we got the answer.
It was a great episode, except for a major issue. We had no idea how it happened, and why only 2, 3 and 4?
Special thanks to creator and Exec Producer JM for telling us what happened. Sadly a scene was cut due to time constraints (need room for commercials). Had it been left in, it would have explained everything.
Before 1, 5 or 6 were ever on the Raza, Portia, Ryo, and Marcus had their neural imprints copied to the Raza by the Android. This is in case she became disabled or shut down, they could still maintain control of the ship.
After the momory wipe, they had no memory of having done this. So when the Android shut down, the Raza activated the imprints, at the time they were programmed into it. This caused the headaches and eventual loss of consciousness.
When they came to, they had reverted to how they were.