I have had this issue on TWO different Kontrol S49s.
The initial firmware update ran for 4-5 hours. I power cycled the keyboard, for a firmware update taking 4-5 hours is absolutely ridiculous. The keyboard then booted into the recovery mode pictured above, and now the installed firmware shows as 0.0.1.
I followed all the steps on ni.de/kontrol-setup, I used the provided usb-s cable as the data cable and I used a power supply as well, even though that should not be needed for the s49. On successive attempts to update I have tried other cables, other power supplies, other computers, even different operating systems. Nothing makes any difference. I have been utterly unable to update the firmware.
Sweetwater kindly responded to my support request, unlike NI for which I have had an unanswered support request open for 8 days!!! Sweetwater sent me a replacement keyboard, and viola, the exact same behavior as the first. I let the firmware update go for over 6 hours and no luck. Power cycled, and back to recovery mode and no path forward.
I have read all the threads regarding this, there is no issue with the driver in device manager on my machine. Sweetwater also reached out to Native Instruments for this 8 days ago, and Native Instruments did not respond to them either.