Why isn't Git tracking changes in a subdirectory?

Try running git update-index --really-refresh.

I did have similar problems on Windows and that solves it.

You should also check the core.ignoreStat option with git config.

Sometimes I have the same problem, especially when I have subfolder which is another git repo itself. The solution is: renaming the folders. Try switching the folder name to something else. Commit that, then rename it back. If the subfolder itself is another Git repo, and you want it to be totally detached from the mainstream, and follow your repo, you should remove the remote of that subfolder first.

So finally it worked. I've removed changed files in local folder - then suddenly git status started to see, that those files are missing. So I've restored them and git status started to see, that files are modified.