1. What decision do you think that John would make if it wasn't the baby that had been misplaced, but a piece of Aeryn's gray matter when reconstituted? And not just inside of Rygel's stomach, but lost on the ocean floor. How do you think the outcome of the mini would have been affected?
2. PK's physical bodies are altered to the point where they liquefy in a wormhole right?
What if it wasn't necessarily the ancients that changed John to be able to hold the tech in his head?
What if the wormhole that brought him altered him enough, changed him physically...although subtly, that it allowed him to affect time in BBBTF? What if 'Jack' saw this while exploring his memories and saw a safety net for the tech as a way to keep things in place once his people reached their destination?
Sooo..the tech WOULDN'T necessarily be gone from John at the end of the mini. He could be some sort of natural depository of wormhole knowledge and Einstein could only remove the wormhole weapon knowledge. Not the actual knowledge itself.