I must be missing something here because any tracks you reorder in the Project Window will follow in the mixer.
In fact, I’ve had this problem in Kontakt when I’m assigning outputs there and forget something.
Contact will not allow you to change the order of it’s outputs (I forget to add a 4th Tom in a very large drum kit, for instance) and I end up adding another output in Kontakt and moving it to the correct position in Cubase instead,
Hugh