I'll explain what had happened with us during those days and what an incredible stupidity we had stumbled upon during those days.
Without any warnings our hosting provider (mochahost) had stopped supporting of InnoDB storage engine. That resulted in like half of our tables to become unreadable=corrupted (since MySQL don't know how to read them without that engine running).
We have realized that fact like in few days after server went down. But before that we've tryed every imaginable way of recovering our database tables to save all the data we had. And we've failed in that, since we needed filesystem access to our base files.