See this discussion for background.
It now seems clear that there is a random bug that accidentally deletes folders and puts them in Trash -- and then may give you a warning message from a new feature, called "Warning: Your Trash is Overflowing". If you then flush the trash, you will never get back folders that in fact you may not have intended to delete at all. It's random.
I and a few others have fallen victim to this and we really would like to see action from Linden Lab on it, but