Thanks for you response Albert,
I think I had 5.1.7 installed at the time but I'm not sure. It would have been a few years old by now. Maybe 4.1.7?
I believe it was express, I know it was free so assuming express was the only free version in the past 2-3 years, that must have been it.
I wish I could reproduce the prompt that I saw. However, I had just opened Express a few days earlier (when I began noticing I couldn't sign pdfs back with OS X 10.11.?) so when it popped up after installing Sierra it looked familiar to me. That is why I believe it was Smart Card Assistant.app. I'm away from my backup disc until Tuesday afternoon or Wednesday morning. I will attempt to go back to the prior Express install using time machine unless you think that is a bad idea. Let me know.
If it helps, I ran the diagnostics with Express 5.3.3 the current version. I can send that to you privately if that helps as well.
Thanks!