Transmission Noise problems of the 2009 Ford Escape Hybrid

In 2012 a clunking noise and slight lurch began to be felt occassionally when breaking my 2009 Escape Hybrid. Over time the clunk and surge increased in intensity but remained intermittent. When I took my vehicle in for its 40,000 mile maintenance, I requested that the dealership check my breaks. They reported the breaks looked in excellent condition. Over the next year the clunk and surge got worse. Suspecting perhaps my transmission or u-joint was the problem, I took the vehicle in to the dealership to diagnose and fix the problem. I was able to leave the car at the dealership for about 1 month. I told them I was not in a hurry, I just wanted it to be fixed properly. Several mechanics drove the car and explored possibilities but reported back to me that it was a normal aspect of the hybrid breaking system although somewhat extreme (more severe than most hybrids). One mechanic explained it to me in this way. There are two types of breaking in the hybrid. In electric mode the car uses "simulated breaking. " in normal engine drive mode, the car uses "normal" breaking. When I use the break, the computer decides which type of breaking is required and when to switch between the systems. Under certain circumstances, when in between modes, the clunk and surge occurs. The abs breaking system complicates the problem. The mechanic suggested I try to drive so that I can break the car more slowly and gently. I believe the degree of clunk and surge is dangerous and may contribute to the hastened deterioration of my car. I am also worried about the breaks actually failing. I am worried that my 2009 Escape Hybrid is unsafe. The mechanics at the dealership insisted there was nothing they could do to fix the problem.