This exact problem had happened to me once while using 3.0. It was a pain because I was lazy with my backups and hadn't kept one for an entire week. I'm not sure what causes the XML files to become corrupt, but the editor will sometimes throw warnings at you before it happens.
Like any piece of software, Stencyl isn't fail-proof, so back up frequently! If that was your only copy of the project, may it rest in peace