If the funds or stock certificates were unclaimed they were forfeited to the State. Once they became the property of the State they have the right to dispose of them in any manner they see fit. The stupid clerk in the comptrollers office who handled the sale probably did not realize what kind of value he was dealing with and sold them at face value. And why should he ?
The proceeds were not going into his pocket. The question now becomes " Did the statute of limitations expire for you to claim these certificates ?" If so, the State had every legal right to take possession and sell them. Since you are dealing with New York State you need, not only a good probate lawyer but one with good political connections. The Judges who are appointed to the Surrogate courts that handle these matters are picked for who they know rather than for what they know. It is a political plum given out for party loyalty rather that for competence.

                                       SOL ZELLER