The NSA has claimed that its systems are "too complex" to stop destroying evidence in pending lawsuits against it. They claim that that stopping the automated destruction of data would have to lead to a stoppage of all surveillance systems in order to facilitate keeping the data the system currently holds.
The problem lies with the vast amount of data that is being swept up by the various NSA programs like Prism, Somalget, and Stellar Wind. The technology to store that amount of data is enormously costly, so the NSA keeps a "rolling cache" of the information that they have retained. This means that data is continuously drawn into databases by the system, and uninteresting or old data is constantly being destroyed by the system to conserve space.
A court order requiring the NSA to retain all pertinent data to a lawsuit would require them to stop deleting information and to hold onto everything they collect leading to a vast overrun of all of their storage systems in short order. Rather than shut down the systems and retain the data as they have repeatedly been ordered to, they have continued to destroy data in violation of the court order.
The destruction of vast amounts of evidence and violation of multiple court orders could dramatically impact the outcome of court cases in involving the mass surveillance programs. One such case by the Electronic Frontier Foundation (A VikingVPN partner!) has had court orders to retain evidence ignored three times.