The mixer is loaded with a series of aux tracks for every Kontakt 6 instance I load.
How can I get rid of these?
Use the cog on the VST instance in the Play Tab, to control the number of audio tracks that appear in Dorico’s mixer for a given instance, if that is what you mean. If you have a single staff or part going to multiple instances - kinda interested in how you did that. 
That did get rid of them. Thanks