Encountered an interesting thing yesterday during tracking - changed my audio metronome setting (just changed the type of sound it was using and DB level) and it wouldn't work after that.  Tried resetting audio engine, restarting Sonar, checked it was still routing properly to the metronome bus and wasn't muted, etc.. all to no avail. 
 
Since I was tracking, I had all FXs bypassed, using the FX bypass button.  I clicked it again, temporarily enabling all FXs and the metronome worked again.  Bear in mind, I wasn't using a MIDI device for an eternal click, I was definitely using the internal audio metronome.  I recreated this issue a few times to be sure - if the disable FX button is enabled, any modification the audio metronome settings causes it to stop working.  Re-enabling all FX (or re-enabling them and immediately disabling them again straight away - either is fine) causes it to start functioning again.
 
Can someone else confirm this issue manifests itself on their DAW?  If so, I'll fill out a bug report.

Perhaps the note of the new sound isn't mapped to that particular synth the met uses?

Nope -  I was using the 'internal audio metronome' option, not a synth mapping.  When changing the settings, all I needed to do to recreate the issue was to change one of the sounds to a sound already working.  For instance - in 4/4, the first click is a higher click and the subsequent 3 are a slightly lower pitch (and I had the first click set at a slightly higher volume to make it stand out).  This is the way I've always used it for years.  Just changing the initial click to be the same sound and volume as the remaining 3 (which were functioning fine), caused it to suddenly stop working.

There have been several reports of the audio metronome unexpectedly going silent, and that togging the FX Bypass on/off would fix it. In those other cases, FX Bypass was not enabled when it happened, so I don't think that's necessarily the cause, but toggling it is the cure.
 
EDIT: Just re-read that you are able to reproduce the issue by changing metronome settings while FX are bypassed. Will check that out; any setting in particular?
 
EDIT2: Confirmed; just changing the First Beat dB level while FX were bypassed silenced the playback metronome. Disabling FX bypass during playback brought it back, but the click was out of sync with the timeline until I restarted playback.
 
Good catch; you should definitely report it as I don't think anyone ever previously identified the cause.

Thanks for confirming Brundlefly - I'll submit a bug report to the bakers.
 

jfyi.. Cakewalk problem report submitted:  CWBRN-68358