There's a fairly straightforward workaround. Control Link only grabs hold of the the controls that you tell it to.
So, I just defined a bank that has the eight knobs configured for different CCs. I have a Keylab 61ii, but I would expect that the Nektar would be pretty similar.
So "Normal Bank" defines the first eight knobs as CC 80-87
Then "Komplete Knobs" defines the same knobs as CC 60-67
So, to switch control modes, you have to switch banks, but that's not too big a deal. It would be nicer if you could just turn Control Link off for Komplete Kontrol, but this isn't that far off from that.
Hope that helps