It doesn't make sense to me that your engine was spewing black smoke and your boost was zero and it was a programming error.
Do the VGT vanes on these turbos have that much control over their operation ? I wouldn't think so, but I know zero about these engines.
If it were my truck, I'd be looking deeper into things. If I had to guess, I'd say your turbo threw a blade and jammed, momentarily. But like I said, I don't know anything about these engines.
I wouldn't be driving it with a noisy turbo until I figured out what happened.