Hi,
Yes, it was possible to switch between optical and thermal. The FLIR Duo has three PWM inputs that can be assigned to different functions in the FLIR UAS app.
What I did was assign three aux outputs on the Pixhawk as RC Passthrough (I think!) and then make sure one of the PWM functions was assigned to the display option. From memory you can have Thermal, Visual or Picture in Picture.
Hope this helps.
Cheers
Mike