I searched for an answer here and on the web and ended up contacting the Wahoo support team.
My Kickr (newest model as of aug 2019) overheated during this workout:(https://www.trainerroad.com/career/emil%20eriksen/rides/64354619-carson)
The solution from wahoo support is:
“I would recommend pointing a fan towards the flywheel from the rear of your KICKR setup to prevent excessive heat building up, especially during high-wattage workouts. When you experienced no resistance during your last interval, this was the KICKR automatically shutting down before it reached temperatures that could damage the unit.”
There you have it - a simple solution if you encounter this problem.
(some words for the search algorithm (Kickr hot, heat, shutdown, resistance drop))