Here is a long story and finally a resolution to the problem.

So I had the turbo rebuilt but the problem returned in a little less than three months. I returned to the shop for warranty work. Being confident in his work and that the turbo should have no problems after the first time he worked on it, the mechanic suggested the problem might be caused by something else. He was suggesting faulty injectors but I find it extremely unlikely since it does not explain the noise coming from the front passenger side of the engine bay. I was also suspicious that he might be trying to come up with some reason to get me to agree on additional work on the vehicle where he can get paid instead of the warranty work that would have been for free. Since we could not replicate the problem (only happens every few months) it was very difficult to do a diagnosis. Anyway, he quickly agreed without much negotiations to reopen and clean the turbo again.

A few months later, the problem returned again. At this point I was almost sure the problem was in fact being caused by something else. I thought, what else could cause loss of power and black smoke in a turbocharged diesel engine? It has to be restriction in the air flow. If it wasn't a sticking turbo, I thought it might be the anti-shudder valve. I did some reading on how the anti-shudder valve works and started suspecting it might be the anti-shudder valve solenoid that's malfunctioning. The solenoid is on the same side of the engine bay where the turbo is found so it might have been the source of the noise. So I came up with a plan on how to do a diagnosis but had to hope that the problem recurs at a time and place where I could safely park the vehicle and look into the engine bay without turning off the engine.

A few weeks later, the problem resurfaced while I was driving only a few meters away from a gas station. I was able to park in the gas station and looked into the engine bay. After giving the solenoid a few hard taps the noise disappeared. I also looked underneath the engine cover and sure enough the anti-shudder valve was in the closed position. Diagnosis solved.

I have replaced the solenoid last December and the problem has not returned since.