No enemies retain protection for long in phase 4, but we still see the "Protection Drain" message appear when protection-less characters damage Nihilus. Based on this message, it appears that Nihilus is still increasing his protection by 25% of the attacking character's protection even after the character's protection bar is empty. If he didn't do this, these protection gains would be meaningless. The skill doesn't say "If any protection was lost this way, Nihilus gains Protection equal to the lost protection." The "Feed the Void" skill very carefully words the protection regeneration to indicate that he only regains protection if minions were damaged. Perhaps Lord of Hunger could be worded a little more clearly?
Using some pretty sketchy estimates, I did a calculation that estimated by the time of enrage Nihilus' max protection could be over 2.5M, which would have him regenerate ~300k protection at the start of his turn. If he only gained protection when debuffed enemies attacked him with protection, then he would probably only regenerate ~6-7k per turn, which is meaningless in a heroic raid. If his max protection is 2.5M, and he manages to feed the void with two minions alive, then he'll regain 500k protection - so definitely avoid that.
