well technically, the phone has a counter which keeps track of unsigned firmwares being installed. currently, your counter is at 0. as soon as you flash an unsigned kernel/ROM/Firmware, it will increase to 1. it wont go back to 0 on installing back an original firmware. You'll also get a triangle with an error message on every boot. Although that triangle can be removed with an app called TraingleAway. On the original
Galaxy S, even the counter could be reset by using a JIG cable. Not sure about the Note II. Maybe there is some method for that too.
But from all I have read at xda,
Samsung guys haven't denied anyone warranty for installing custom firmware etc. Even when there was a leaked kernel with the eMMC bug for the Note I which if you flashed basically killed the phone, most people posted that they gave the phone for RMA and the motherboard was replaced even though technically, it was their fault.
But no, you won't lose any functionality(apart from the proprietary Samsung apps) and the triangle on booting on doing all this.
EDIT: just checked, TriangleAway can reset the flash counter back to 0 as well, so you should be fine.
https://play.google.com/store/apps/details?id=eu.chainfire.triangleaway