I've never seen anything like that before.
My best guess at what happened is that the tiny nick on the heatpipe was just large enough that it allowed an air bubble to form rather than being filled in by paste, and that exact spot on the GPU die happened to be somewhere that was a hotspot, but also didn't have a temperature sensor near enough to it to make the GPU throttle. Basically, I think you were the victim of a perfect storm of bad luck.
As for what to do, unless you just recently bought this RTX 2060 Super and can RMA it, I think you might be out of luck.
You could try downclocking the GPU to see if you can improve stability at the cost of framerate. Maybe at a lower clockspeed you'll be able to find an island of stability where the issues stop.
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