Gradient fills do not rotate nor flip horizontally or vertically. Thus, when you rotate or flip a gradient-filled object, the gradient will be unchanged.
The gradient will appear as if it still has the same "light source" as the original. This may mean that oval or circular objects with gradients focused on their centers may have their gradients appear to be off center when flipped or rotated. You may need to create new gradients with different focus points to fill the rotated/flipped objects.