The trial was stopped for the second time in 2010 because of the prosecution's refusal to disclose the name of one of its witness intermediaries.
As for the case's other defendant, Mr. Kozlowski, "he would have been killed" if he had testified because of the prosecution's portrayal of his lavish lifestyle.
The case had garnered widespread attention in part because of the prosecution's use of secret evidence against Mr. el-Atriss.
President Obama, Mrs. Clinton and other senior officials explicitly warned Egypt's military leaders that the aid this year was at risk because of the prosecution of the American-financed organizations, which include Freedom House, the International Republican Institute and the National Democratic Institute.
But the litigation has also drawn attention because of the prosecution this summer of Mr. Kissel's brother, Andrew M. Kissel, on charges of engineering an elaborate real estate fraud in the New York metropolitan area involving tens of millions of dollars.
Spell said the DA's inaction forces him to pursue appeals that will argue that Phipps, who has served 16 years of his 30-year sentence, should be freed or given a new trial because of the prosecution's legal bungling.
Because of that, the prosecution decided there was no reasonable chance of conviction.
In many cases, the exculpatory evidence surfaces only on appeal of a conviction, and often comes to light because other aspects of the prosecution are rife with error.
Mr Ibrahim had sought to have the charges dropped because a member of the prosecution team was involved with the man who accuses Mr Ibrahim of sodomy.
But investigators in some of the many agencies involved in the hunt for the suspects, all of whom spoke on the condition of anonymity because of the pending prosecution, have provided some details.
