For reference I upgraded to ICS from stock rooted GB via the following:
1. Plugged in stock rooted GB note to Win7 64bit PC using factory USB cable.
2. Started Kies and it requested to update the firmware for the Note.
3. A total of two progress dialog boxes appeared with downloads.
4. After the downloads, The Note was automatically put into Download mode and the firmware dialog progress started.
5. After the progress dialog completed (2-3 minutes) the phone rebooted and went into the typical ICS "Optimizing x of x Applications" dialog box.
6. Everything completed after that and obviously root was gone but everything previously was intact and ICS was good to go.
Also I used the non flash counter increase 500+ MB root process when I was running GB stock.