I have a Visual Studio solution inside a git repository created with TortoiseGit version 1.8.16.0 (git version 2.6.2.windows.1)
I just updated Visual Studio from 2015 to
I had the exact same issue as you and spent hours trying to get it to work, including re-cloning.
I solved it on my end by adding the *.VC.opendb and *.VC.db files to the .gitignore file of my project.
As soon as I returned to Visual Studio all my pending changes were showing. As far as I can tell it's all working normally again.