Let me share my story with the update, it may help others.
I instantly updated my Kontrol S61 keyboard with 2.0.4 firmware after I saw that there is a new version available in the NI newsletter. → first mistake
After it installed (it takes 2+ hours every time) only the basic functionalities worked, so I saw only the default midi template on the keyboard screen and the black and white keys worked and nothing else. After when I tried everything on my computer I selected Settings → General → Reset on the keyboard to do a factory reset. → second mistake
It made everything much worse because after reboot the keyboard stuck on the serial number screen, because it was not able to communicate with NI Access. I tried to connect it to another windows computer but the same thing happened.
The issue was that NI Access did not installed the new version of Hardware Connection Service correctly (or at all).
The solution is to search Hardware Connection Service and install it manually from here as timrae_NI mentioned in another post: https://www.native-instruments.com/en/account/downloads/
Now everything is working fine, but it was really a bad experience.