Running Ubuntu and Pillars of Eternity (patched to 1.3) under Steam.  I loaded a game (started before the patch if that matters) and added a new companion--a fighter--to hold the line and at some point during a battle at Caed Nua and noticed he was no longer wearing any clothes.  I opened up his inventory and sure enough he was missing his chest armor and large shield.  I retraced my steps on the map wondering if it was a game mechanic (like a disarm from an enemy), but didn't see any place he could have dropped it.  I opened up my load menu and jumping back to the autosave where I entered Caed Nua it was already missing.  

 

Odder still, I shrugged it off and ran back to repurchase armor for him.  I went to the blacksmith and purchased a new set of armor and a shield for him.  After completing my purchase the armor and shield were nowhere in the stash or inventory, yet the money was taken from my purse.  I don't know how I can use this companion if I can keep things equipped on him.  

Posting here to confirm that this is a problem. Playing on Windows via Steam, using a fully custom party. Party was created post-patch. Noticed at some point that my paladin and cipher lost their weapons. Re-equipped them, thought how odd that was, then ended up going back to Gilded Vale only to notice that my monk lost his clothing. I'm not sure what triggers it exactly, but fear of losing actual important items is keeping me from playing right now.