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Out of the box, I installed Samsung 960 Pro in M.2 slot 1 and Crucial SATA SSD in slot 2 and installed Windows 10 including the latest updates.
Then, went to Intel and downloaded all latest drivers. I started by upgrading the Bios, which was a year old, but Windows won't boot anymore.
I went in the Bios to find that the Samsung is no more detected. I reset the Bios, tried to downgrade it but nothing works. I then switched the disks' slots just to test if slot 1 is still working and realized that NUC now sees both! Removed both disks and tried a Predator PCIe SSD in slot 1 but still not detected. Moved it to slot 2 and it was fine.
In short, what I have observed is that M.2 slot 1 lost PCIe protocol following Bios 0050 upgrade.
Opened a support ticket with Intel 36 hours ago but still no reply so far.