I can think of 3 without any knowledge of a specific case. Potential Delay (in clarifying this matter against the case at large), Proof of Effort, FISA routinely allows for incomplete filings and go forward anyway. They aren't the only court to do this. Pope's publicity might help squash this, but it's up to a judge to allow it or not. After the information is garnered, an appeal court can overturn it and nobody can undo the discovery. Any lawyer, can probably come up with more. I'm not explaining every obvious tactic. My advice is to get familiar with how far the US intelligence community has fallen out of jurisprudence. Good Luck.
your comments above sound reasonable, but your characterization of tech dirt as a rumor site is wrong in my opinion. They consistently find cases of government overreach and attempts to skirt the law. If anything, they'd be supportive of your comment above "My advice is to get familiar with how far the US intelligence community has fallen out of jurisprudence."
How does that explain the strange behavior of submitting a document in such a state though? Couldn't they have achieved any of those goals by submitting the document without the annotations?