Here's a quick post before my tip gets lost in Twitterverse. After enjoying a good upgrade experience, I went to use my pen for my Surface Pro 3 and it wasn't responding. The first thing that occurred to me was the right thing - pair your pen again.
— Darrell Webster (@DarrellCWebster) July 29, 2015
2. The Connect pane appears on the right side of the screen.
3. Hold down your pens top button for 7 seconds till light flashes
4. Second message appears in Connect pane, "confirming" the pen is connected.
5. Try the pen in your favourite inking app. Mine is @ ... of course :)
Here's the instructions from Microsoft's Surface support site
It's good to see the pen clicks still working well. I opened the OneNote app with a single click of the top pen button.