I'm not sure what might be the cause of the problem, can you please try to perform the following and check whethet it will help to fix the error you are getting:
1. Shut down JIRA
2. Delete the content of $JIRA_INSTALL/work directory
3. Delete the content of $JIRA_HOME/caches/indexes directory
4. Delete the content of $JIRA_HOME/plugins/.bundled-plugins directory
5. Delete the content of $JIRA_HOME/plugins/.osgi-plugins directory
6. Start-up JIRA
7. Perform indexing
I hope that will be helpful.
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