If your mom bought it as a rifle, but had issues with it being slated a handgun, then the FFL didn't know his laws very well. How it comes into inventory and how it is sold is what dictates their records. 4473's and inventory records are NOT classification docs, so if he received it as a rifle and sold it as such, it doesn't matter that it could be rebuilt as a pistol. The current configuration is what matters for inventory and transfer record. She shouldn't have to have gotten a permit to purchase for a rifle.

If it wasn't barreled, then it would have been an "Other." Not a handgun. But that does require, in some states, the same permit to purchase as a handgun.