I have no idea- I have over 5K sites, and 200 from around 4 different hosts (just some from each host) all got de-indexed at the same time. I haven't done anything over the top with the sites, they were all small sites with unique content, good external links (none of them were linked together). For backlinking I don't do anything big- just around 2-10 backlinks per day from article directories and social bookmarking mostly, but a small amount of scrapebox and profiles. They are small sites so maybe they got a manual review and looked like mfa sites- but I wouldn't think that would get them de-indexed.
They also had a tag cloud with keywords and the keywords were linking to blank pages, other then that we had the downtime/blank site issue for about a day and after that that giant number got de-indexed.
We also had about 5 pages of unique content and 5 pages of auto content that we have removed now just in case. It just doesn't seem like we did anything very drastic to attract that kind of negative reaction, but I guess the things above could have caused it? Very frustrating.