Dr.
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It depends on what you mean by upper. The ISS, for instance, is technically located in the thermosphere (part of the upper atmosphere). But for practical purposes, we typically say that its in space (not in the atmosphere).If a spaceship was flying in the upper level of a planet's atmosphere, would taking out its engine bank cause it to crash to the planet surface, or just immobilize it?
If your spaceship is within the conventional atmosphere - behaving like an airplane, using its engines to stay aloft - then shooting out those engines would cause it to fall (or, at best, to glide to a crash-landing). If it was in orbit (as Doc Evo mentioned), then its engines wouldnt even be on. A sci-fi type boarding raid would be much easier in orbit than in atmospheric flight.