They have the same meaning, but the first is more emphatic for me.
Student or Learner
66 In the early days of my first web hosting company, I was often criticized for "not sticking with plans." If I saw a better opportunity, I would often divert all energy to the new opportunity and let the other one go. It's like being on a busy sidewalk and seeing a dollar bill a few yards away; you start to walk toward it with the intent to pick up, and then you see a ten-dollar bill that is even closer. How could you not change course and pick up the ten-dollar bill instead?
What is the difference between the two? Is 1 more emphatic as "not" is closer to the verb "change"?
1. How could you not change?
2. How couldn't you change?
1 is also more common and sounds more natural.
At least in AusE, one would say "How come you couldn't do X?" or "How is it that you couldn't do X?" rather than "How couldn't you do X?" But the meaning here is different. It relates to something not done in the past. Your example is hypothetical - "How could it be that you would not change course?"