I have this strange problem in Jenkins 1.5.31 .
I had configured Maven jobs which I still see in Jenkins_Home directory. My Jenkins Windows service was not getting s
After Jenkins restarts, there is the case when some jobs are missing if the syntax in their config.xml contains errors.
When all errors are fixed the job should appear. You can validate your configurations against some online tool, f.e.: https://www.xmlvalidation.com/
Another case is when all Jenkins jobs are missing and an empty dashboard is loaded. This indicates that Jenkins home directory is wrong, so make sure to specify JENKINS_HOME correctly and restart Jenkins.