Rest assured, your upgrades have not disappeared. Some upgrades are currently inactive to make way for new foods in the second chapter of the Food Truck.
 
You can view all active and inactive foods in your Food Upgrades tab. Here, you will also notice any foods or stations carried over (such as eggs or the stove) have retained your upgrade levels.
 
 
You may also notice some previously purchased foods are locked. These will automatically unlock, along with any associated stations, once the newer foods have been unlocked. Any previous upgrades made will be retained, as well.