Chances are you installed a windows update to your server that caused this to occur. There was some in April and May 2016 time frame that were released.
Completing the post installation tasks will resolve the issue:
Microsoft Warns WSUS Users About Flawed KB3148812 Update
I had this issue twice now on the same surface.
The issue is the keyboard and the trackpad will not work, all troubleshooting was done including replacing the keyboard with the Surface Pro 4 keyboard and still no luck.
Just shut down the Surface Pro/2/3 normally using the power button. Then, when it’s off, press the power button and the volume up buttons at the same time, for at least 15 seconds. You may see the screen or the lighting on Type Cover flicker, but keep holding the buttons.
Release the buttons, and let the machine sit for at least 12 seconds. Then, turn it back on normally.
Your system might enter the system bios, just use the keyboard to exit. After booting into Windows your keyboard should work fine again.