This is an FYI for anyone having this trouble as much as a bug report. After spending several hours working on a piece yesterday (and saving frequently), I opened Musescore this morning to find that everything I worked on yesterday was missing. I searched the save files and the autosave backups to no avail. After much searching and panicking I discovered what happened. It turns out that the file had been saved properly just in the wrong spot. Instead of overwriting the previously created file in the score directory, Musescore saved it under a bizarre name in the home directory (I'm using Linux). But my work was safe so if you're having a similar trouble it might be worth searching you computer for .mscz files and see if they wound up in weird places.
It looks like instead of inputting the path correctly, Musescore replaced all the slashes with underscores which dropped in the home directory.
Version 2.0.1 for Linux
OS Fedora 22