Wow! That is really bad news.
I'm trying to figure out how this could have happened so that I can avoid a similar problem in the future.
Did you create a new "folder pair" or did you try to use the existing "folder pair?" If you used the existing folder pair, I'm wondering if the program became confused by trying to sync with a secondary drive that it could not properly identify.
If I ever find myself in the same situation that you faced, I will definitely make a unrelated backup and then try the "contribute" mode to avoid any deletions.
Thanks for the heads-up.