After saving some modifications to a job, the job configuration page started being incomplete, showing correctly just the first configuration items, but showing an error message for the last ones.

I went to see in the jenkins_home directory and found that the whole configurations had been lost and rewritten by a git clone of the repository used by the job I was modifying.

Unfortunately I can't give much more detail because all the configurations that led to the breaking were lost. I do have recovered the working configurations from a backup and I can provide info from there.