What she said. Oh Crap.
I don't know why I was still using the slightly older SG version. And stupidly, I last backed up more than a week ago.
It was either CB 1759 (I tried it briefly, Spout 681 spat errors so I shut it down) or CB 1772 (when we all noticed the voids).
It seems to have deleted all the stone (ID:1) in those chunks.
... now i have the fun job of restoring map chunks with MCEdit or something....
I am very worried about trying Stargate again until I can track down and eliminate the source of this problem :/
EDIT: after digging throug older server logs, I think I found where and when it happened.
My first trial of CB 1744. It deleted a pile of Pavement (ID:1) by a stargate, which would have been when it
also deleted all the stone. It also tried to delete all the stargates I use that have stone as the gate-closed item.
I'm getting no such problem on the Creative server (CB1772, Spout 686. The same gate format works fine.
Dev builds of bukkit. Gotta love em.