I think you are seriously overthinking this. Its very simple. They CAN save data. Period. How do I know? Its very simple here. Do you really believe that if they found credible data on a top Con Queso leader, that they would need to analyse it within a specific time frame before they lose it forever, or do you think they can flag it to be saved?
Perhaps a bit less simple if you consider the breadth of the judge's order and understand the ramifications of being on the wrong side of that order by later being found to have (however unintentionally) deleted any data inside its scope.
Being able to save the small discrete pieces of data in your hypothetical has nothing to do with whether they could fully comply with the court's order, which prohibited them from “destroying any potential evidence relevant to the claims at issue in this action , including but not limited to prohibiting the destruction of any telephone metadata or ‘call detail’ records , pending further order of the Court" (emphasis mine). In short: until further notice, save everything.
Without even getting into the question of whether the systems have the capability of archiving every bloody bit without some sort of manual intervention, as others have already observed, the sheer storage space required to carry everything along gets really big really fast after you exceed the age-out window you designed into your system. The discovery process in civil litigation doesn't exactly run at a breakneck pace.
And even if you were to try to save it all by making the necessary architectural changes and slapping on storage capacity, if you screw up and lose any data whatsoever in that process, that quite often will result in an instruction to the jury that they can presume the data you destroyed would have proved the other side's case. There's generally little point in following through with a trial at that point -- the outcome is nearly certain with that kind of a thumb on the scale.
I'm far from a fan of the NSA, but I get why they spoke up quickly and loudly about this. To say nothing now about the prohibitive breadth of the court's order (i.e., to signal that they intended to comply) would just make it worse for them were any data lost down the road.