The answer is simple: have multiple backups all the time, but without immediate syncing.
If you try to import a package to Unity in improper format (like I did it with a 4.2 prefab to a 3.5 Unity Pro), your whole project is f…ed up without any alert. No any pop-up like ‘Not compatible format’ or something…. just a crashed application.
Then you cannot use your whole project anymore.
Well done, Unity Team. AAA engine, you say…