It appears that somehow, JIRA/JIRA Agile is able to get into such a state that the Epic-Story Link is duplicated in the issuelinktype table of JIRA database.

The following SQL query returns more than one row from database:

SELECT * FROM `issuelinktype` WHERE linkname = "Epic-Story Link" 

Symptoms

• JQL queries using linktype will break (See: https://confluence.atlassian.com/jirakb/advanced-search-for-has-epic-link-type-fails-in-jira-server-779158623.html)
• JIRA and JIRA Agile are unable to retrieve Epic Link data or Epic associations i.e. all issues or stories would appear missing from their epics (See: https://confluence.atlassian.com/jirakb/all-epic-link-data-appears-to-be-lost-779158624.html).

Expected Behaviour

• JIRA/JIRA Agile should be able to prevent or detect and delete this duplicate linktype entries.

Not quite sure if this should be a JIRA or JIRA Agile issue, but I'd leave developers to decide and move this if necessary. It occurred in a JIRA 6.1.4 instance.

Workaround:
Please find workarounds to fix the broken data in the KB article links provided under the Symptoms section above