Wouldn't they have receipts of what they bought from the manufacturers? It would be a simple matter of comparing the invoices from manufacturers to purchase paperwork, then adding in the current in-store inventory...
they (the ATF) inspect your "bound book" in which all transactions must be recorded. As a small dealer selling only 50 to 75 guns a year I can attest that it is easy to make a error in the book. The ATF will go back to the manufacturer of a gun used in a crime and look to whom it was shipped. You had better have your I's dotted and your T's crossed as the ATF will not have mercy on you.