Edit: I just reloaded an older game and the problem exists when I had just arrived at the Holomayan Monestary. The save prior to that is a fair bit older so I can't say exactly where it happened. Any ideas? I know I didn't drop the items in question, because it would have taken a very deliberate move to do it. Between loads I lost all of my grands, greaters, and petty soul gems, filled and unfilled, but kept all of my common and lesser ones.