One way would be to re-initialize the remote repository completely cleanly and then do a push from local.
On the server, in the directory where the bare repository should live, do
git init --bare
On the client (local repo), set the new origin if it has changed, and push to the server, and set up tracking again.
git remote set-url origin <Remote_URL> git push origin master git branch --set-upstream-to=origin/master master
Sources
http://stackoverflow.com/questions/23397089/how-to-restore-git-bare-repository-from-local-one