If the plugin doesn't work on 5.0.4 another option might be a Jelly script scheduled via a service as mentioned in the comments at https://confluence.atlassian.com/display/JIRA/Re-Indexing+after+Major+Configuration+Changes
Since JIRA 6.1, it is possible to trigger a re-index via the REST API:
If you wish to schedule it for a particular time of the day, you may create a script which triggers the re-index via the REST API during the scheduled time (e.g. via a cron job).
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