Last boss atlas tree points not available after using book

I was at 6/10 on the boss atlas tree when I killed the Arbiter. Two atlas books dropped (arbiter and boss) but I wasn't able to assign the boss points and still showed as 6/10.

I've since completed a T16 irradiated boss map which gave me another two points which put me up to 8/10.

Do I need to kill Arbiter again to get the last points?

The quest is no longer available in my quest log.