Not getting skill points for atlas tree (bosses)

Good day!
When leveling up the character Sichiha, I received 4 skill points in the atlas tree (map bosses). When trying to kill another boss, my character died, but after that the boss was killed by my minions. The boss dropped an atlas skill book, which I could not pick up because I was dead. Now I can't level up this atlas branch further, because there are no necessary perks (+1 to the boss difficulty level).