So if you plan on scaling out Jenkins with slaves and the like you’ll probably want to ensure your configuration is kept someone secure, handily there’s a plugin for that.
Jenkins SCM Sync - which to be fair I have a bit of a love hate relationship with and since building up a new Jenkins server last week hasn’t got any better, the config loaded in fine, but then would error on every save / change.
So a new week and time to hit google and I found the answer of how to get it working again within the detail on issue Jenkins-25786 which is basically manually push the changes in the local git repo.
sudo su jenkins -s /bin/bash
cd ~/scm-sync-configuration/checkoutConfiguration/
git status # see untracked files
git add -a
git commit -a -m "fix all the things"
git push origin master