From what I understand, this can happen in Unity (not just to PlayMaker), but don't think there's a lot a developer can do about it. It might be worth searching on UnityAnswers -I seem to remember people talking about this, and someone might have written an editor script to re-attach missing script references.
If not, I can look into an editor script for this when I have some free time...
EDIT: Also using some form of version control and a backup system should minimize any lost work when things go wrong.