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I was having a problem with all of my build history getting repeatedly deleted -
JENKINS-23067. I noticed that the buildsdir directory was non-standard. I changed it back to the default value and have not seen the issue since. In my case it was set as follows-<workspaceDir>${JENKINS_HOME}/workspace</workspaceDir>
<buildsDir>${JENKINS_HOME}/workspace/builds/${ITEM_FULLNAME}</buildsDir>
(I didn't set it up originally, so I couldn't guess as to why)
I am not sure that this was the issue, but it also made the thinbackup plugin correctly back up the history so I won't lose it if the problem does resurface. The deletion seemed to happen very early in the morning, perhaps on a server restart (if that helps in any way)