If search engines are indexing your site with any regularity and you kill all your DNS records I'd say it's not terribly surprising to have your domain removed. That combined with the new .org being an exact match for a "cyanogen" search would probably do it.
It looks more likely that someone form the search team browses HN or uses Cyanogen (very likely) and they intervened and updated the index manually. I am sure google has a back-end to do stuff manually.
The .com site did completely disappear, and for a relatively high profile site like that, it's probably indexed pretty often.
There's also the possibility that the developers had access to the "Google Webmaster Tools" for cyanogenmod.com, even though they didn't own the domain, and so just told Google that the site had moved.
It's the #1 on Bing and DuckDuckGo as well, though interestingly you can still see links in the .com in both Bing and DuckDuckGo results, but Google has eliminated the .com completely from their results.