What DAW are you running? Run us through exactly what you did.
Two tips:
1) Sequential saving - Avoid using "Save" and use "Save As" instead. Then, when you're saving, put a number after the title. Eg "Song - 1", "Song - 2" etc. This way, if you make a mistake, you can revert to an earlier version and start again. I "Save As" about every 15 minutes when I'm working on stuff.
2) Back up, back up, back up - Can't stress this enough. If you have a major fuckup, it's always nice to have a backup. Always back your sessions up to a separate drive (such as an external - or if you use an external to work on your stuff elsewhere, when you get home back it up onto your computer).
I had a drive fail on me a few months back, lost about a weeks worth of work. I had the stuff backed up and it was all stuff I could redo (audio editing), just left it too long before I backed up again. Whereas, if I never had it backed up, that would have been one very angry band. Nowadays I work off one external drive, and when I'm finished, I save my work and back it all up to another external drive. I then back up to my computer every two weeks or so. Just good practice
Edit: Just noticed this is in the Pro Tools forum

Still, point out to me what you did. There should be a folder in your session folder called "Session File Backups". Go into that, and look at all the date/times and find one that was made before you lost your audio. Open that session, and then save it as a regular session (Pro Tools doesn't like you running "Recovered" session files as a regular session).
However, this all goes out the window if you had "Session Backup" turned off - but I doubt you did. Because, if you did turn it off, you'd know it was there and you wouldn't be asking the question

Hope this helps.