The clean-up feature of Cakewalk/Sonar starts by finding all Cakewalk/Sonar data files (*.wrk, *.cwp) on your hard drives. It then looks at each data file and identifies which audio .wav files are being used by it. Then, it lists all the .wav files which are not associated with a data file and lets you delete them.
You could try backing up your audio directories and letting the utility run. Sorry to sound ambivalent, I misread your question the first time.