The old scary Knock sensor issue.
Couple of ways with Nistune to verify functionality of knock sensor, doing a street tune. The 3rd gear long pull will not always show the best results. A fast run-up in second gear to high RPM (record the run) will show you if you are going into the knock map. I am going to try another method, which will have the car static at 2000 RPM and creating a false knock (brass hammer to engine). Deleting the knock sensor or radically changing the map is not an option here.
I am curious about your tune, and your setup. An aftermarket system for knock detection will show you a problem, but its an after the fact input. Tuning requires real time data. Just like the old oil pressure light on the dash, if its lit your probably causing damage.
PM me if you want to talk via phone.