When I first add a project to source control(GIT) it will show all of the files and everything will be peachy. I can continue to work for about 30mins-1hr and all of the change
I found VS was holding an .opendb file open, causing a permissions clash when searching for changes. It reported the precise file that was causing the trouble in the Output window, under "Source Control - Git". Adding this to my .gitignore fixed the issue. If a VS restart or a reboot fixes the issue then you're probably closing the offending file handle -- in my case VS opened the problem file every time.
See also Visual Studio TFS Git not seeing any changes for more potential causes.