Have you done any preventative maintenance stuff like deleting preferences or repairing disk permissions? It's not that complicated and it sometimes works for projects that don't have corrupted files in them. Just go to
Mac HD > Users > (your home folder) > Library > Preferences > com.apple.iMovieApp.plist (move it to the trash)
And fire up Disk Utility and do a quick Repair Disk Permissions, reboot and open iMovie and see if the project's still lost the audio track.
It almost sounds like it's messing up the Autosave it peforms in the background as you work on the project. My feeling is you could also test this by opening the project, make one edit. Quit iMovie. Re-open iMovie and see if it's also keeping track of edits properly.