I am using Git in VS2013 and my changed files are not showing up in the Changes window of VS.
When I have changed a file but before I have saved it to disk it does show
I had this problem too. It happened randomly, and sooner or later my git status was completely erased from Microsoft Git Provider add-in in Visual Studio, although it was correct on Git bash.
Turns out that, in my case, it would happen as soon as I open a connection to a LocalDb database from SQL Management Studio, and kept the connection open. So, I suspect this might happens whenever a process locks out a file which is monitored by Microsoft Git Provider.
Hope it helps. In my case, it's fixed!