I ran into trouble when I wanted to link two JIRA instances together using the Application Links feature. It would always give me the following error message:
This application has the same ID as myself. Can't create link to myself.
I actually found a solution in Atlassian's Confluence (http://confluence.atlassian.com/display/JIRAKB/Setting+up+Application+Link+results+in+ServerID+already+being+used) but it seems to be outdated.
I wrote the following query to find the string in a JIRA 4.4.1 instance:
SELECT * FROM [jira_db].[jira].[propertystring] WHERE propertyvalue like '____-____-____-____'
Just edit it and restart JIRA.
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