I’m playing the game online with my dad. He goes and respecs his tree and lost all skill points completely. They were not refunded. And on top of that in a middle of a mission he loses all his loot from inventory completely.
He’ll need to file a support ticket which will at least let the team know of the issue. Not sure what else to suggest at this point.
If he has PSN cloud sync enabled, he could try deleting the local save data and re-downloading the cloud save - if that was an earlier save he’d at least get most of his gear and progress back.