... and I posted a
long post on the BBS explaining my testing and findings.
Anyway, the short story is, food inventory seems to disappear when:
1) a Sim goes to restock and there isn't enough to complete the restocking and then
2) the Sim makes more of same food.
The workaround is to always make sure you have enough of each item when restocking. Otherwise, the next time the Sim makes that item, a "phantom restocking" phenonemon occurs, and the number of items that were not stocked will disappear from your Sim's inventory.