Are you saying you lost all your food or only selected food?
If you lost all your food, you have encountered a quick sale when you blocked your door. The food sold off quickly when you opened the doors again.
If you were saying that you lost selected food on your counters, rest assured that the game does not remove selected food. You might have stored the counter and lost the food in the progress. Or maybe when the game combined your food, check your bakery very closely and see if your food was on an "hidden" counter block from your view, hiding behind a decoration or something.