I think the idea behind the rules was that this couldn't happen:
"Yes sir, we have reason to believe you have terrorist training manuals on your hard-disk"
*search*
"Nope, none found, but we did find some music which the RIAA might be interested in, some videos the MPAA might be interested in, a particular movie Voltage might be interested in, also you said a rude joke in a chatroom which was not properly filtered and marked for adults only"
*lawsuits to death*
But now it can :)
No - the rules were intended to prevent a repeat of what *did* happen:
1. Feds get a warrant to obtain drug testing records of 10 specific baseball players (based on actual evidence against those 10 players).
2. Judge specifically limits them, saying that they have to separate out the records of everyone else, and only keep the records on the 10 specific players.
3. Feds ignore judge's limits, getting records on hundreds of individuals (not limited to just baseball players). No attempt is made to separate out the records on the specific players.
4. Feds then use the info on other players (that they previously had no reason to suspect) to issue supoenas for evidence against those additional players.
What's really scary about this whole mess is that the government is relying on the "in plain sight" doctrine, which basically states that if an officer observes something that is in plain sight during the course of a legal search, whatever the officer observes can be seized and used as evidence even if it wasn't listed on the warrant. For instance, if they're searching your house on looking for stolen goods, and they see your stash of pot, they can seize it and charge you with possession.
But once you have access to a computer, pretty much anything on it is readily accessible (unless encrypted). So applying this doctrine to digital searches ends up being analogous to getting a search warrant for a specific set of (dead tree) files, and then claiming that *all* of the files in the file cabinet are now "in plain sight", and as such they can browse them to their heart's content.
The court *did* uphold that the supoenas, and any information resulting from them, were invalid. But by removing the specific guidelines the earlier court had created, they've opened the door to a repeat performance of this whole mess. Which you can bet *will* happen fairly quickly.