Found it.. It's when you give healing potion to the magister in the prison that's being interrogated by the houndmaster. Instead of getting just one potion he gets an entire stack. I had 14 minor healing potions in my inventory before I started the conversation with him and after giving him "a" healing potion I had 0, he drank all 14 of them.
Though.. I do not think it only happens there, I've notice entire stacks of potions go missing in the Hollow Marshes too.
Sorry for coming across as an ass in the OP, but seriously.. Your track record for breaking stuff when you're "fixing" stuff with the Divinity Original Sin games isn't making you look good. :\
Last edited by Skeptical_Bunny; 03/12/18 03:14 AM.