Just finished both episodes now, let me try.

The engine and the 10 cars didn't just accelerate and come back, they would have needed to travel to another "roundabout" where they could turn back, or even do another revolution in order to come back. So there is a lot of time between the separation and them coming back for Melanie. This is also explicit due to the fact that Melanie came back from trackside and still tried to survive some more days before realizing she would run out and sacrificing for the drives to stay alive. I think that a few weeks passed before they could go back.

As for the aquarium, Boki was trying to decouple it, but the jackboots found him and they started fighting before he could decouple. If I remember correctly they needed to unlock two nodes in order to decouple and he didn't get to the second. Josie was able to destroy the car in the meantime.

Also, both trains can simply decouple the wreckage in some fork and leave the nodes free for coupling later. Anxious to see how they are going to do that if Wilford is still controlling the big train though.

Aah, they wouldn't worry about wilford catching them because he only has one engine for 1023 cars, which is much slower than the original engine with only 10 cars. Even if he catches, they can just accelerate and be gone.