Pillars of Eternity is a lovely CRPG, but it's a lovely CRPG from Obsidian Entertainment, a developer that's be known to miss the odd bug or two. Like the one that strips your character's permanent buffs and abilities if you double-click equipment in your inventory.
The relatively devastating bug, posted to Reddit by kiror yesterday, happens when a player tries to swap out a piece of equipment on a character with an item in their inventory by double-clicking the inventory item—a relatively standard role-playing game practice. Doing so will remove a character's racial abilities, passive powers and permanent buffs.
You can see a clip of the bug in action here. I tested it with my starting character, swapping out a looted leather chest piece for the default chain, and my racial ability disappeared immediately.
While players are reporting that dismissing NPC party members and then re-adding them to the party resets their passive and racial buffs, others claim that doing so triggers another bug that removes all items from the NPCs' inventories.
Other players are using the game's built-in cheat console and the "addability" command to rebuild their characters' abilities. Note that using the cheat console disables Steam achievements.
Obsidian is aware of the issue and have a (hopefully retroactive) fix already made, but have to extensively test any update before it's rolled out, just in case they screw up the game again.