They would have had to work it from the manufacturer's records.
The gun was only in production a few years, so there couldn't have been a large number of them out there. Factor in eliminating exported guns, and guns shipped to distant states, and the number to look for becomes more manageable. ATF gets a list from Charter saying this many went to NY, this many went to NJ, this many went to PA, etc. Send a memo to the ATF field office in each state and send the G-men out in search of...
This was a high-profile case that made national news. I'm sure they had an army of agents working the case.