Hi ReginaLiz,
I don't know if you already found a solution to your problem. I downloaded the upgrade to 4.3 about two weeks ago and started having the same problem with S Note a few days after the download. I kept trying to open S Note, by touching the home screen an also the app icon on the apps screen, and it would not work (have some very important notes on that app that I couldn't afford to lose!).
I then pulled the S Pen out, which opened a blank note, scribbled something on it and then saved it. When I then tried to open S Note, it was working again. I honestly don't know if it was because of the S Pen or what, but I have not had any more problems.
Hope this helps,
Ana