The second microphone next to the camera is for noise-cancellation which doesn't work when you use the loudspeaker or headset.

The mic used for calls is the one located at the bottom. N9's speaker and mic are weaker in general as compared to Nokia N8's for example, so maybe the receiver can't hear you properly if you hold the phone a bit far away.

However, if it completely "stopped" working, it could be a hardware or software issue. Maybe you can do a reflash and try again before pointing it to a hardware issue.

Edit: some research shows that a possible reason for the mic to stop working can be due to debris that might have been collected in the mics. So if you blow some compressed air in the two mics, it might work again. Try not to clean it by poking things inside.. then it'll definitely be a hardware issue.