It's not the preservation of the data that's the problem, it's the collision of civil procedure discovery rules with natioanl security issues: The EFF had wanted the NSA to preserve all data collection in bulk, regardless of what legal authority it was collected under — that way, the government would be forced to hand it over as part of the discovery process as the case moves forward.

In general, disputants in civil litigation have to provide complete transparency. If I sue you over a business matter, for example, you have to provide everything that you might have on record in relation to that business matter, not just those documents which are responsive to my initial complaint. My lawyers will then pore over those records and file an amended complaint that makes maximum use of your information against you. In turn, your lawyers will almost certainly counter-sue me and make a similar request for my documents on the matter, to find out whether I know something that you don't. This is completely different from a criminal warrant, where the state has to articulate in advance waht it's looking for (although such requests can be fairly broad).

The reason it works this way is because civil itigants are ofen at a severe disadvantage. If I have a bad experience with BigCorp and sue, I don't know in advance what specific documents or records to request for evidence, because I'm not privy to BigCorp's inner workings, have no insight into which BigCorp employees or managers were involved with the situation or what actions they took, and so it would be very easy for BigCorp to give me the runaround - an experience most people are familiar with if they've ever had a problem with a bank or received poor customer service from a large organization. So the civil discovery process is designed to correct that imbalance by giving a plaintiff's attorney access to all the same information as the defendant's attorneys, and allowing plaintiffs to amend their complaint for greater specificity after the discovery process. (Of course this system can be abused too; some defendants will deliberately swamp a plaintiff with far more information than actually requested, in order to leave the plaintiff's attorney's looking for a needle in a haystack. Attorneys usually contract out that research task and after the verdict is passed down there is often further litigation about the appropriate assignment of expenses.)

Now, of course the discover process can involve a defenedant having to hand over a great deal of information that is not relevant to the actual dispute, with negative implications for privacy and business confidentiality. But since attorneys are all officers of the court, they are bound as part of their license not to make public any information they receive which is not responsive to the matter being litigated. For example, suppose a plaintiff's attorney discovers that the CEO of BigCorp is having an extramarital affair, but that fact isn't germane to the litigation. The plaintiff's attorney would be subject to severe sanctions, maybe even disbarment, for leaking or threatening to reveal that information at trial in hopes of causing embarrassment or jury bias towards BigCorp.

So here the EFF is saying (as is normal) 'give me everything you've got, our lawyers will sort through it and cherry pick it for relevance.' The NSA is arguing in turn that it can't do so because the EFF's legal team doesn't have the relevant security clearances, and that the public's security interest eclipses the public's transparency interest - which may well be true, in Constitutional terms. A lto of people liek to argue that the Constitution, or more specifically the Bill of Rights, exists to protect the people from government tyrrany, but the BoR is only part of the constitution and doesn't automatically trump other parts. The Constitution also grants a large number of powers to government and the legal authority derived from that stands on an equal footing with the public's interests that are articulated in the Bill of Rights.