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Martin: Recent Jenkins versions (1.507+) are considered to no longer lose information on running builds when reloading, see
JENKINS-3265. This warning (now) exists primarily to prevent accidental reloads that make the Jenkins UI unavailable for several minutes (especially with larger instances).I experienced some build data loss in combination with 'Cloudbees Restart Aborted Builds Plugin' (Jenkins Enterprise) but without that plugin, have repeatedly and successfully reloaded configuration from disk without losing in-progress build information.
If you're on a recent Jenkins version and lost data, you should probably file a new issue and provide more information about your environment.