What was destroyed and why? Those answers are redacted, but here's a theory based on nothing but my own speculation.
Ackerman and Carol Rosenberg point to Judge Pohl's December 2013 order to preserve CIA black sites abroad as the most likely relevant preservation order. If that is true, the redacted defense motion released today says that about six months later there were secret ex parte communications between the government and Judge Pohl as a result of which Judge Pohl "authorized the government to destroy the evidence in question."
One possibility is that the "evidence in question" was specifically the remnants of the CIA black site in Poland at Stare Kiejkuty and the "why" was the release (or pending release) of two European Court of Human Rights decisions -- seven months later in July 2014 -- in Nashiri v. Poland and Husayn (Abu Zubaydah) v. Poland that found Poland violated the European Convention on Human Rights for failing to carry out a real investigation into the torture of detainees at the CIA black site, thus obligating them to undertake one that might finally include collecting forensic evidence from that black site.
To flesh the theory out a bit, if six months after Judge Pohl's Dec. 2013 preservation order -- in about June 2014 -- the U.S. government acquired intelligence that the European Court of Human Rights would soon find Poland in violation of its legal obligations under the European Convention to conduct an effective investigation into the CIA black site; and if the U.S. knew that Poland could therefore no longer play along with the U.S. in delaying and obstructing an internal Polish criminal "investigation" -- on the back of which Poland had refused to provide evidence to the Court -- that had been going nowhere for years; it would not be a stretch that the U.S. would go to Judge Pohl ex parte and say that the CIA needed to destroy the remnants of the Polish black site because failing to do so could result in evidence falling into the hands of uncleared Polish investigators creating a U.S. national security issue, potentially providing actual confirmation of the black site which the CIA had studiously avoided, and creating political and diplomatic problems for U.S. relations with the Polish government to whom the U.S. had made promises of protection.
Moreover, the prosecutors could have argued for the ex parte nature of the discussion by stressing the sensitive nature of intelligence about the result of a pending court decision and the foreign affairs concerns that could not be shared with the defense.
Just a theory. Katherine Hawkins at the Constitution Project also had an interesting theory that it was a black site in Afghanistan.
Apologies if anyone has already advanced the ECHR theory and I missed it and I will edit the name of this post to "A Quick, Discredited Theory" if and when it is shown to be wrong..@charlie_savage I think it's prob BROWN in Afghanistan, only one whose confirmed existence stretches into protective orders taking effect— KatherineHawkins (@Krhawkins5) May 12, 2016
UPDATED to fix a typo.