(sorry for butting in on Neil’s behalf)…
I think his previous comment refers to the Nano Editor and the Nano Kontrol sometimes not communicating… not about general usage 
.
Like I said, once you have made your changes to NanoKontrol, you no longer need the Editor (it worked, with its current settings, before you’d even downloaded the Editor, didn’t it? )… it has its own (guessing: EPROM?) memory.
Set up the NanoKontrol, using the Editor (and Save … in case you need to reload it at some time), with Cubase closed. Quit the Editor. Launch Cubase. Normally, you should never need to even open the Nano Editor again, unless you want to make further changes.
Yeah - that’s what is not working here 
Can you at least get this far?..
With Cubase closed, open the Korg Editor. Is the NanoKontrol at least seen as online?
If so, can you change the CC# for fader #2?
Can you Save it?
Close the Editor.
Reopen it.
What is the value for Fader #2? As original, or with your edit taken into account?
If it has reverted to the original, reload the file that you had just saved. Has it correctly taken into account your edit?
With Cubase closed, open the Korg Editor. Is the NanoKontrol at least seen as online?
Yes.
If so, can you change the CC# for fader #2?
Yes.
Can you Save it?
Yes.
Close the Editor. Reopen it. What is the value for Fader #2? As original, or with your edit taken into account?
As original.
If it has reverted to the original, reload the file that you had just saved. Has it correctly taken into account your edit?
Yes it has.
I’ve just opened the Korg Editor here, and there is maybe one step missing… Does the PC version have menu items, “Communication>Write Scene Set”, and “Communication>Write Scene Data”? (can’t remember now the difference between a “set” and “data”, but, it does look like you have to employ these in order to transmit the modifications to the NanoKontrol itself).
Fingers crossed, but I think that may be it, at last! .
EDIT: I’ve just checked the documentation, to see the difference between “data” and “sets”… your NanoKontrol v2 may not even have “sets”, just “data”. “Data” is all the… errm… data corresponding to your faders, knobs and buttons. “Sets” applies to v1, where there are four different “scenes” (the “data” is the info for a scene, and a set is the combination of all scenes).
Anyways, see what “Communications” options there are for you… I’m sure it will be clear .
That’s it! 
Thank you so much! If you weren’t so far away, I’d kiss you! 
Ah… distance can be a wonderful thing, sometimes! 