I am also experiencing this issue. The only way I have been able to effect a fix is to switch to a full shutdown instead of hibernating. This issue was introduced with a recent Microsoft update.
For those experiencing this issue it is easier to set your surface to shutdown rather than disabling/enabling the pen via the device manager, taking the battery out or repairing. All of these work but it's a real pain to do this every time the surface is
resumed from hibernation.
The problem is easily reproducible by setting the surface to hibernate. Every time the surface is restarted the pen button will no longer function.