Just like you would delete any file.
Rather than messing with just the metronome directory, you might be better off, reinitializing SONAR. While there is a copy of the audio metronome files in Cakewalk Content, there is another location that is the basis of your local copy used by the drop down in SONAR. Try this, Start SONAR with the CTRL+SHIFT keys pressed. This will re-personalize SONAR, copying a bunch of files including the metronome files into the correct location.