I have this problem too. I installed the Windows 10 Creators Update and it does not work.
But after installing the Creators Update I have uninstalled the Radio Card from Device Manager (right click on Radio Card > Uninstall) and rebooted Surface (Pro 4).
In the boot fase he tells me he's updating.
After the "update" the Pen works.
I hope this solution may be useful for you. Thanks.