This issue happens extremely often to me due to the fact I start Arma 3 with the mission file parameter without loading the correct mods, I then get distracted and over 5 minutes later I remember that I opened Arma 3 then alt-tab back in, the autosave sound plays, and the mission has been overridden by the now empty mission.

According to Dedmen ticket please, auto save should be disabled while "missing mods" dialog is open.