I have a root folder with a git/ folder and one submodule (mymodule). mymodule has its own git/ folder, too.
git status shows:
# modified mymodule (untracked content)
Then I have removed a git folder from the submodule, and now if I change something in mymodule, it doesn't show with git status. 
git add mymodule doesn't work.
All mymodule changes are untracked.