Today I lost an important database. I asked in #aegir and omega8cc and ergonlogic experienced the same thing.
omega8cc told me that it can happen in edge cases where a half baked clone is deleted, and the settings.php file still has the old credentials. That can make the site being cloned loose it's database. It happened to me, and it has happened to both omega8cc and ergonlogic also.
Might I propose that the settings.php is altered before being put into the cloned site?