No, there is not a known issue that could lead to config.xml being removed.
None that I know, though if you allow jobs to run on the controller (because you have at least 1 executor enabled on the controller), it is feasible that a rogue job could delete files on the controller. If you have made that mistake, refer to the Jenkins documentation:
Your Jenkins controller file system may have been damaged or overwritten or reverted to an older copy. When Jenkins fails to load a plugin, it is usually because a dependent plugin is missing. Your best path is probably to restore from backup.
That is a very old Jenkins version, that is no longer supported by the Jenkins update site. So it might have happened that you have one plugin that is too new for you Jenkins that fails to load and that then takes down a whole bunch of other plugins.
I strongly recommend that you update to the latest Jenkins LTS version and update all plugins as there are several security issues reported.
I would suspect that the ionicons-api plugin is too new as the version 88.va_4187cb_eddf1 requires Jenkins 2.479
So check the Jenkins logs for the first occurence of a failed plugin
If the workflow-job plugin can’t be loaded all pipeline jobs will not be loaded and look as if they got deleted. The config.xml files are likely still there.
Also not that your command ls -ltr $JENKINS_HOME/jobs will not list config files but only the directories in the job folder. The config.xml files are one level below