Words like "clothing," "strip" and "buff," when placed together, would usually form a pleasant sounding sentence. Not in Pillars of Eternity, though. Its sentence is downright terrifying: a game-wide clothing bug could strip your party of their passive buffs, permanently.
This malignant curse appears to be widespread. As detailed in this Reddit thread, it happens if you double-click to replace the armour or equipment of your character. The workaround is to instead drag-and-drop items to their slots. It's easy to avoid, then, if you know it exists. If you do trigger the bug, you should be able to reload a save and restore the buffs—although, who knows how much progress that might cost.
In a forum thread, you can find plenty of speculation about the nature of the bug as well as potential solutions for the afflicted. For instance, it seems as if it's possible to restore an NPC party-member's buffs by removing them from your party and adding them back in.
Obsidian has acknowledged the bug. "We do have a fix for this," writes lead programmer Adam Brennecke, "and I'm trying to make it retroactive, so it will fix any save games that have this problem."