Manually delete application link from JIRA database
https://confluence.atlassian.com/jirakb/how-to-remove-application-link-directly-through-jira-database-285839519.html
If you need to do the same for confluence:
https://confluence.atlassian.com/confkb/alternative-methods-of-deleting-application-links-in-confluence-316637672.html
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