Since the forum won't let me reply to the original question, here goes:
Q: Got the Note 3 Lollipop update yesterday. Now my S Pen doesn't work properly. How do I fix it?
A: Yohanna, you might be better to look on some of the Android fan sites for info on this, as there are a small number of participants in this community who would have experienced issues with updates. If you find an answer, please join in the community by sharing what you learn.
Thanks for your reply. I checked some Android sites yesterday--and they all pretty much say the same thing. Do a 'factory reset'. I have to admit, I'm resisting that option. The last time I switched phones, it took about a week to get it set up back to where I had it... However, it looks like that's my only option....