Thanks to Chris I was able to fix this by running the following:
git filter-branch -f –index-filter ‘git rm –cached –ignore-unmatch pi/data/node-login.0’
git filter-branch -f –index-filter ‘git rm –cached –ignore-unmatch pi/data/node-login.1’
git filter-branch -f –index-filter ‘git rm –cached –ignore-unmatch pi/data/local.0’