Use the Brute Force Method: Turn Off All Ringtones
Options | Ringtones and Sounds. Now you need to set ringtone for the various ways you might receive a call to “None”. But remember with this method you will not get an audible ring on any incoming call.
Turn off the Lync 2nd Incoming Call Waiting Tone
Options | Ringtones and Sound and Check “Keep sounds to a minimum when my Status is Busy”. This will make it so that a 2nd (or more) incoming call waiting tone will not be played.
My Headset Is Still Playing a Call Waiting Tone (beep-beep-beep on a 2nd call)
Check with the headset settings, most of them can be configured. You may need to install the vendor specific tray application to change the settings.