Symptoms
Adding fields to a SmartObject that is generated off of a SharePoint list lead to the fields being deleted upon regeneration.
Diagnoses
Adding fields to a SmartObject that is generated off of a SharePoint list is not recommended, as upon regeneration your fields will be deleted. This is expected as to keep the SmartObject in line with the SharePoint list.
Resolution
It is recommended to either add the columns to SharePoint and then regenerate your SmartObjects, or create a new SmartObject that isn't tied to a SharePoint list.