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He would have liked to use all the non-infringing content that was there as evidence that Megaupload was a genuine cloud storage company.

completely uninformed here, but wouldn't having the servers wiped be better for the defense? no evidence for him, but none for the prosecutor either.

The prosecutors already had copied whatever evidence they needed from the servers.

And he's now unable to prove that the "evidence" isn't faked, since he can't access the servers himself and verify the contents.

At the very least it should make a good case for an appeal.