The volume level in the Lync app will set the system volume to the same value as the app. Adjusting the system volume is not reflected in the app. At some point, the app will again set/reset the system volume. This causes a problem if you are wearing earphones and have adjusted the system volume down, when the reset happens it can be... unpleasant.
Separate app volume from the system volume. Consider the system volume as the max volume possible and don't change the system volume from the app. The volume slider in the app can then be used to offset the volume relative to the system volume.
80% system volume with 100% app volume = 80% volume
100% system volume with 80% app volume = 80% volume
This would also follow the convention of other apps like iTunes, internet videos, etc.