You can fix your repository by rebasing the changes of your private repository on top of the remote changes.
- add a new remote to your repository containing the correct remote git URL.
- fetch from that remote to fetch all the correct remote commits to your own repository
- use
git rebase
to transplant you commits on top of the remote commits. - merge your branch into the remote one.
This would be something like:
cd $your_git_repository
git remote add origin $URL
git fetch origin
git branch -m my_branch
git rebase --onto $base_commit $your_first_commit my_branch
git merge $remote_branch
git log --graph --decorate --oneline
where $base_commit
is the commit corresponding to the zip you downloaded in the first place, and $your_first_commit
is the commit you commited the extracted zip file as.