Can I isolate a part of my movie (for example the sky) over time, and give this part another color. The problem is, that the cut of the sky is changing (not always the same size, panning shot).
You’ll need to make a duplicate layer and then mask out the sky (sounds like you will need to animate the mask as well) and then apply the appropriate image effects to get what you want.
But, if all that you’re doing is changing the color of a region then try the Change Color effect. You may need to create a garbage matte if there is much of the original color in the rest of the shot.