@chrisp7
After reading your post I understand that may be messing with tracker was the culprit in my case. One day Gallery on my N9 was not updating images, newly shot images were not appearing there. So I tried to restart tracker and everything was OK(I do not remember the exact command I used, and it is way too back in my history).
After that I was using the phone for more than a week, when I had to restart it. That is when the contacts, messages and call logs went missing.