Strange. Assuming you have enough farmers your food stocks should have recovered fairly quickly. In cases when I've had an event or the gong takes all the food in the past I've dropped every available villager in the ocean and the bin is looking quite healthy again after half an hour.

There have been occasional reports of mature villages suddenly losing all their food for no apparent reason while closed - there may be a rare _bug_ that happens so infrequently that it it is difficult or impossible to pin down. However, that doesn't explain why the food stocks didn't start building up again.