Have you installed the latest driver for the Audio Kontrol? If so, maybe try a re-install?
http://co.native-instruments.com/?id=freeupdates
I’m not sure what else to suggest. It should show up in the ASIO Driver selection dropdown I would think. Very strange. Especially since you had it working successfully in the past.
As far as the projects go that are showing the missing ports when loading, are these old saved projects from when you had it working properly? What happens when you start a project completely from scratch?