Another idea is to smith ~100 iron daggers, improve them, and then place them in his most used chest. Improved items do not stack, so he'd either have to pull 100 daggers out, or withdraw all and then deposit everything back in.
EVEN BETTER! Take all of his stuff, then place it in one sack and then put the improved daggers in it! oh and enchant iron armour and name it "I know what you did" and put it on top of the chest.

I like that.
I would simply ask..... and say that you know the house is bugged and was wondering if he moved stuff or if it was "lost in space".
My Husband and I played Red Dead Redemption with the same umm file. I liked gambleing, collecting flowers and finding the hidden treasures. Huge sums of money were gone cause he liked hunting and had to buy ammo. And while I didn't care I can see where it could get bothersome.