How do I deal with False Son post rework?

[Fishious]

It's been a short while since I've played ror2, this is the first time playing since the boss rework and I remembered it being quite bad prior to the update. While fighting him it was all going fairly well until phase 3 where he still has that attack which takes away your abilities. I broke some geodes but my abilities didn't return like they usually would pre-rework. How do I actually handle phase 3 if I can't get them back with geodes?