But once an organ has evolved, you can't simply get rid of it. Amphibians only make sense if they had to adapt to a swamp environment, which I guess didn't exist in the shuttle. Also why would these changes begin after their flight, and without any new generation? It just doesn't make much sense in terms of evolution.
Did you follow the link to the article?
"Cave fish dwell in perpetual darkness, are generally blind, having either greatly reduced eyes or no eyes at all. Yet presumably they evolved from fish with functioning eyes. Why lose the ability to survive in other niches? Researchers have put forth two theories. One holds that unused functions can accumulate destructive mutations without affecting the creature. The other theory posits that unused functions get dropped in order to redirect the energy involved in maintaining them, enhancing useful functions. New research published in the journal Nature supports the latter idea."
Organs do vanish. So don't limbs. You can read about whales and manatees and all sorts of land mammals that returned to the sea and lost their limbs. You can read about mole rats and cave fish that dwell in perpetual darkness and have lost (or are losing) their eyes. An organism adapts to it's environment.
I don't know why the show had them evolve into "salamanders", Its science fiction, and they had to evolve into something. But the notion of them evolving into simpler life forms because there was no environmental stimulus makes sense. Worm-like creatures might have made more sense, since everything would go... arms, legs, eyes. But the salamanders were more interesting.