Trouble is, you wouldn't be able to patch a section of WAV into a 5.1 AC3. If DE can figure out a way to do this programmatically (and he is damn near genius at C as his edit proves) then that may be a solution. But otherwise, it's a matter of demuxing the disc and remuxing with the corrected AC3 file, which is an entirely different file as far as computers are concerned.