Will it affect the rooting on my note 3 if I update?
Sent from N9005 4.4.2 NB7 rooted device
You should turn off Automatic Security Policy Updates in Settings -> General -> Security.
Uncheck Auto update Security and depending on your usage, disable or enable Via Wifi Only so that it doesn't constantly ask.
They could patch some KNOX stuff and certificates in these updates, so you wouldn't want it if you're rooted.
Grabbed photo from AC: