I have configured the plugin as follow:

• Use different history directory than default:: [Empty]
• Max number of history entries to keep: 20
• Max number of days to keep history entries: 365
• Max number of history entries to show per page: [Empty]
• Configuration exclude file pattern: queue|nodeMonitors|UpdateCenter|global-build-stats
• Do not save duplicate history: ON
  
  * Save Maven module configuration changes: ON
  
  * Show build badges: Always
• Exclude users: [Empty]

Now to my amazement, I found on the FS files like:
drwxr-xr-x 6 lthy ne 4096 Nov 11 2016 home/config-history/jobs/testJob_deleted_20161111_152741_018
drwxr-xr-x 6 lthy ne 4096 Jun 29 2016 home/config-history/jobs/testMultiBranch_deleted_20160629_190653_773
drwxr-xr-x 8 ltphy ne 4096 Aug 30 2016 home/config-history/jobs/Try1_deleted_20160830_093601_349

So this looks like the job got deleted in 2016. (I have similar cases for later years.)

With "Max number of days to keep history entries: 365" I would have expected everything deleted more than a year ago to be removed.