Certain folders cleared by something

I had symbolic links setup to an external drive in my home directory for templates and documents, and somehow my screen flashed and these folders were cleared. Fortunately I had some backups, but what caused this and how can it be prevented?

Edit: Now my system does not seem to recognize the folders as the templates and documents folders, even though I did nothing to changes them.

Edit2: It appears to have bumped all the contained files up a level to my home directory as well…