The court gave the verdict on Wednesday while ruling in an application filed before it for the declaration of Dotun Babayemi as flag bearer of the opposition party.
The trial judge, Justice Binta Nyako, said she too was just saw the new charges this morning and rejected the plea of the prosecution to go ahead with the case.
After his release, he began hosting supporters who throng his residence in solidarity before army personnel stormed his home and opened live rounds, killing dozens in the process.
The amendment came on a day the trial judge, Justice Binta Nyako fixed to hear the bail application of Kanu, pending the determination of the charge against him.
The defendants, Bilyaminu Aliyu and Aminu Hukunci, all pleaded not guilty when docked.
The appellate court added that Mr Edede did not establish any cause of action to have warranted his approaching the court on the issue because he did not establish that he was directly affected by the provision.
Justice Mohammed ordered that the defendants be put on notice of the motion for them to respond by showing cause why the prayers sought by the plaintiff should not be granted.
The apex bank boss filed the lawsuit at a federal high court in Abuja, the nation's capital, a move that has now confirmed he is interested in running for the political office he denied declaring for at the weekend.