Not even the concept of positive and negative (cancellation of momentum) can be attributed to clockwise and counterclockwise. It is the magnitude of the arc motion; and how they interact; not the direction. When you have two fly wheels that are touching or geared to each other one is going clockwise and the other is moving counterclockwise; yet if you try to stop one they will work together to resist the applied force. It takes a careful evaluation to properly apply the concept of vectors.
The 4.5 (total mass) to 1 (sphere) mass cylinder and spheres has a cylinder motion of 1.2 m/sec clockwise at the end of the experiment and at the beginning of the experiment; but in the middle the motion (3.5 kg * 1.2 m/sec) is stored counterclockwise. The spheres have a continuous motion clockwise; but they will stop the clockwise motion of the cylinder and then restore all of its motion counterclockwise. The spheres will then stop that counterclockwise motion and fully restore the cylinder motion clockwise. At the end you have exactly what you had at the beginning; 4.5 kg moving clockwise at 1.2 m/sec.