I downloaded bittorrent sync to mess around with and see if I could get it working, and when I set up the folder I noticed my file extensions had changed. I checked that my files were there (they were), and saw that all their extensions had changed. After seeing if I could access them from anything else (I couldn't, they were read-only for some reason) I decided to uninstall BitTorrent Sync...and everything went with it. Everything. I immediately reinstalled it to check all the archiving that might exist - since I saved settings - but I'm completely screwed, right? Considering my external just blew out, guess I need to see if I can somehow restore all the data in some other way...it's a pretty massive loss.
