One of the informers has been dropped from the new indictment, which also names six of the seven officers from the earlier indictment.
Faced with the new indictment, the court has decided that the case's trial judge should first decide whether to dismiss the earlier indictment.
In the earlier indictment, a person who turned out to be Mr. Padilla was identified only as an unnamed co-conspirator.
The earlier indictment named several other men, identified by prosecutors as mid-level managers in the Genovese family.
An earlier indictment had merely summarized the meetings covered by the Weinberger notes, leaving the notes themselves for the trial.
At the time of the earlier indictments, lawyers for the officers called the charges unfounded, saying the inquiry was politically motivated.
The earlier indictment was based on events dating back to March 2003 and included charges of kidnapping, stalking and threatening his estranged wife.
The charges in the earlier indictment are misdemeanors.
The daughter is named in the earlier indictment as one of four "no show" employees who, it said, were on the Senate Democratic minority payroll.
Beatrice was not mentioned on the earlier indictment, but sources have said that it is one of the stocks under investigation for the expected new indictment.