Is the Base URL for JIRA set correctly? This needs to be set correctly if you change the configuration for the application.
https://confluence.atlassian.com/adminjiraserver071/configuring-the-base-url-802593107.html
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I'm really not sure here. Have you tried a full re-index? I'd probably consider opening a support issue with Atlassian or digging through the database myself. This seems pretty strange.
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