Nihilus doesn't take any damage on Phase 4 of the Heroic Sith Triumvirate Raid

You're probably right, not the first time ability text has been a bit ambiguous/wrongly worded.

The whole setup is a bit weird then, the idea comes across as Nihilus is draining your protection & taking it for himself, so when your out of protection it seems like he's stealing it from out of thin air, or from the past.

Bit like the tax man.