The stock update is supposed to check to see if the phone shows any signs of ever having been rooted and, if so, to "fail". You can make changes while rooted (that remain even after you unroot) that can brick the phone if you update it.
Normally, you run the phone rooted for whatever reason you want then, when an update comes out, you rlash the stock ROM, update, and root the updated ROM. (So make sure there's a root method for the updated ROM version for your particular model phone [not just Note 4, but your model and carrier of the Note 4] if you want to stay rooted.)