Apparently, HN does have a long-discussion filter which kills threads if they get too long. (although I've never seen this happen on Snowden/NSA threads, oddly enough.)

I'm not a fan of it.

That might make sense for the second thread but the first only has 72 comments and these two disappeared in quick succession.

That story is currently ranked #44 (second page). I don't think it'd take more than a few users flagging it to get that rank given it's also 9 hours old.

It was at the top of page 1 when it suddenly popped off after a refresh.

Between being #1 and you refreshing, one or more people clicked the flag link. That's exactly how it works, no?

No, not with posts that high and that many upvotes. It would take a lot more than 'a few flags' and it would step down the page after every flag. The other thread had 900+ upvotes, it would take a lot of flags to get rid of that one and even 300+ upvotes would take more than just a few.