So, if I understand correctly, we practically need to locate the broken workflow linked with that issue somewhere and add this post function "Re-index an issue to keep indexes in sync with the database." ? Am I misunderstanding something, or is there a way to figure out which issue has to do with the inconsistency?
We had the same issue when we added our custom code to Jira which threw NullPointerException(NPE). In this case the reindexing did not take place and lucene index was inconsistent. Maybe it is your case as well, look for NPE in the atlassian-jira.log.
Actually this situation could be caused by any unhandled exception in a custom code which try to create or modify issue.
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