I just wanted to *Bump* this discussion as I came across the issue as well, but was able to resolve it using another method. I experienced the issue in a project still ongoing in Civil 3D 2011. I wasn't able to purge regapps/purge all/audit and save successfully as mentioned above or any of the other methods, unfortunately. Civil 3D also wouldn't allow me to successfully SAVEAS with a different drawing name in the same server directory.
However, I was able to save the file to my workstation hard drive, close and perform a RECOVERALL, and then copy the file back to the server. I then reopened the file and performed a QSAVE just to test if the alert message came back, and fortunately it did not. Hope this helps someone else.