I had the same with my previous GT160 (supercharged/turbocharged). That made it the most unreliable car I ever had after 5 misfire breakdowns-quite simply it was dangerous. Iirc, the car went through 2 sets of different spark plugs, 2 or 3 engine maps, 2 sets of fuel injectors. If even got connected up live to the factory. After all that (from only 2000 miles old) I still wasn't convinced as I could detect a slight misfire the very next day after a week in Germany-that was the final straw for me, I traded the car in at VW and pushed for goodwill at VW UK
Worth bearing in mind, on some cars piston damage could occur. The misfire was/is a known problem
Sorry for the potential bad news. I would think by now a fix has been found, mine was 4 years ago
Hope you get it sorted, please keep us updated