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That's an interesting report. I'm not aware of any case where the repository is wiped (which would remove the .git directory and the .gitignore file) without either a job configuration which says the workspace should be wiped, or a user action to wipe the workspace. Does it happen with any other job than the specific job which shows the problem?
Do you have a history of the configuration of the problem job? Does that history show any significant change at the time the repository was wiped?
Do your users have the permission to use the "Wipe out workspace" link that is usually available with each job? Could one of the users have chosen to wipe out that workspace?