Having removed the aquaero and reinstalling the farbwerk on its own I could get it to work after a firmware update. I then removed the farbwerk and did the same to the aquaero. Finally I reinstalled the farbwerk to work alongside the aquaero (both via separate USB cables) and all seems to be well.
Why it didn't work the first time, I don't know. I'm just glad it's all up and running again.