Symptoms:
Duplicate Agile Board error is reported by Integrity Check, but such board is not accessible through JIRA's UI and produces a similar error:
Cause:
Agile board's visibility is based on its filter's JIRA Share Permissions, not on administrator privileges. https://confluence.atlassian.com/adminjiraserver071/managing-shared-filters-802593150.html
A user can create a filter and not share it and it won’t be accessible by anyone, admins included. Modifying the board owner and boardadmins tables won't help either, it's the share permissions that determine a filter's visibility.
Resolution:
Use the following Groovy script to make all filters on the system global:
...